Starting phenix.real_space_refine
on Wed Jan 15 10:17:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xq4_38565/01_2025/8xq4_38565.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xq4_38565/01_2025/8xq4_38565.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xq4_38565/01_2025/8xq4_38565.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xq4_38565/01_2025/8xq4_38565.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xq4_38565/01_2025/8xq4_38565.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xq4_38565/01_2025/8xq4_38565.cif"
  }
  resolution = 3.21
  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=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    5375      2.51       5
     N    1365      2.21       5
     O    1451      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8237
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1044, 8237
          Classifications: {'peptide': 1044}
          Link IDs: {'PTRANS': 32, 'TRANS': 1011}
          Chain breaks: 5
  Time building chain proxies: 5.53, per 1000 atoms: 0.67
  Number of scatterers: 8237
  At special positions: 0
  Unit cell: (83.16, 112.32, 123.12, 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      46     16.00
     O    1451      8.00
     N    1365      7.00
     C    5375      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: 2.21
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 4 sheets defined
      75.0% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 75 through 95
      removed outlier: 4.277A  pdb=" N   VAL A  79 " --> pdb=" O   PRO A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 120
      removed outlier: 3.914A  pdb=" N   VAL A 105 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.678A  pdb=" N   HIS A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 153
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 155 through 162
      removed outlier: 3.505A  pdb=" N   SER A 162 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 189
    Processing helix  chain 'A' and resid 194 through 207
      removed outlier: 3.807A  pdb=" N   ALA A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 220
    Processing helix  chain 'A' and resid 223 through 253
      removed outlier: 3.749A  pdb=" N   GLY A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   THR A 228 " --> pdb=" O   LYS A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 292
      Proline residue:  A 276  - end of helix
      removed outlier: 3.837A  pdb=" N   HIS A 292 " --> pdb=" O   PHE A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 318
      removed outlier: 3.895A  pdb=" N   GLU A 300 " --> pdb=" O   ASP A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 337
      removed outlier: 3.703A  pdb=" N   ALA A 326 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 375
    Processing helix  chain 'A' and resid 381 through 412
      Proline residue:  A 408  - end of helix
    Processing helix  chain 'A' and resid 418 through 428
    Processing helix  chain 'A' and resid 432 through 447
      removed outlier: 3.659A  pdb=" N   LEU A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY A 447 " --> pdb=" O   GLU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 481
      removed outlier: 4.383A  pdb=" N   SER A 453 " --> pdb=" O   ASP A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 513
    Processing helix  chain 'A' and resid 522 through 530
      removed outlier: 3.682A  pdb=" N   ALA A 526 " --> pdb=" O   ASP A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 558
    Processing helix  chain 'A' and resid 571 through 600
    Processing helix  chain 'A' and resid 604 through 619
    Processing helix  chain 'A' and resid 639 through 652
      removed outlier: 4.186A  pdb=" N   TRP A 643 " --> pdb=" O   GLY A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 676
    Processing helix  chain 'A' and resid 679 through 705
      removed outlier: 4.278A  pdb=" N   VAL A 693 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      Proline residue:  A 694  - end of helix
    Processing helix  chain 'A' and resid 727 through 753
    Processing helix  chain 'A' and resid 754 through 760
    Processing helix  chain 'A' and resid 761 through 784
    Processing helix  chain 'A' and resid 798 through 853
      removed outlier: 3.856A  pdb=" N   ALA A 816 " --> pdb=" O   ARG A 812 " (cutoff:3.500A)
      Proline residue:  A 819  - end of helix
    Processing helix  chain 'A' and resid 853 through 858
      removed outlier: 4.019A  pdb=" N   MET A 857 " --> pdb=" O   ILE A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 889
      removed outlier: 3.663A  pdb=" N   HIS A 889 " --> pdb=" O   LEU A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 919
    Processing helix  chain 'A' and resid 923 through 943
    Processing helix  chain 'A' and resid 952 through 959
    Processing helix  chain 'A' and resid 960 through 964
      removed outlier: 3.960A  pdb=" N   ALA A 964 " --> pdb=" O   SER A 961 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 977
    Processing helix  chain 'A' and resid 1043 through 1050
    Processing helix  chain 'A' and resid 1069 through 1080
    Processing helix  chain 'A' and resid 1085 through 1107
      Proline residue:  A1101  - end of helix
    Processing helix  chain 'A' and resid 1113 through 1122
    Processing sheet with id=AA1, first strand: chain 'A' and resid 979 through 982
      removed outlier: 6.230A  pdb=" N   GLN A1064 " --> pdb=" O   VAL A1002 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989
      removed outlier: 6.534A  pdb=" N   VAL A1057 " --> pdb=" O   ILE A 988 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126
      removed outlier: 6.553A  pdb=" N   ARG A1185 " --> pdb=" O   ILE A1148 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ASP A1144 " --> pdb=" O   VAL A1189 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137
      removed outlier: 3.924A  pdb=" N   ASN A1154 " --> pdb=" O   GLU A1159 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   GLU A1159 " --> pdb=" O   ASN A1154 " (cutoff:3.500A)

    618 hydrogen bonds defined for protein.
    1833 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: 2.76

  Time building geometry restraints manager: 2.54 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2593
        1.34 -     1.46: 1560
        1.46 -     1.58: 4159
        1.58 -     1.69: 0
        1.69 -     1.81: 83
  Bond restraints: 8395
  Sorted by residual:
  bond pdb=" C   LEU A 143 "
       pdb=" N   PRO A 144 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.36e-02 5.41e+03 3.06e+00
  bond pdb=" CA  ILE A 818 "
       pdb=" C   ILE A 818 "
    ideal  model  delta    sigma   weight residual
    1.523  1.539 -0.016 9.20e-03 1.18e+04 3.03e+00
  bond pdb=" C   ILE A 488 "
       pdb=" N   PRO A 489 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.022 1.28e-02 6.10e+03 2.84e+00
  bond pdb=" C   THR A1100 "
       pdb=" N   PRO A1101 "
    ideal  model  delta    sigma   weight residual
    1.336  1.356 -0.020 1.23e-02 6.61e+03 2.72e+00
  bond pdb=" N   THR A1157 "
       pdb=" CA  THR A1157 "
    ideal  model  delta    sigma   weight residual
    1.460  1.484 -0.025 1.54e-02 4.22e+03 2.56e+00
  ... (remaining 8390 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 11192
        2.33 -     4.67: 151
        4.67 -     7.00: 27
        7.00 -     9.33: 11
        9.33 -    11.67: 3
  Bond angle restraints: 11384
  Sorted by residual:
  angle pdb=" C   VAL A 741 "
        pdb=" N   ILE A 742 "
        pdb=" CA  ILE A 742 "
      ideal   model   delta    sigma   weight residual
     121.97  129.80   -7.83 1.80e+00 3.09e-01 1.89e+01
  angle pdb=" N   ALA A 679 "
        pdb=" CA  ALA A 679 "
        pdb=" C   ALA A 679 "
      ideal   model   delta    sigma   weight residual
     114.56  109.24    5.32 1.27e+00 6.20e-01 1.75e+01
  angle pdb=" C   HIS A1156 "
        pdb=" N   THR A1157 "
        pdb=" CA  THR A1157 "
      ideal   model   delta    sigma   weight residual
     122.46  128.30   -5.84 1.41e+00 5.03e-01 1.72e+01
  angle pdb=" C   HIS A 677 "
        pdb=" N   MET A 678 "
        pdb=" CA  MET A 678 "
      ideal   model   delta    sigma   weight residual
     121.54  129.02   -7.48 1.91e+00 2.74e-01 1.53e+01
  angle pdb=" N   ILE A 413 "
        pdb=" CA  ILE A 413 "
        pdb=" C   ILE A 413 "
      ideal   model   delta    sigma   weight residual
     108.82  104.33    4.49 1.22e+00 6.72e-01 1.35e+01
  ... (remaining 11379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.10: 4576
       16.10 -    32.19: 349
       32.19 -    48.29: 75
       48.29 -    64.39: 21
       64.39 -    80.48: 4
  Dihedral angle restraints: 5025
    sinusoidal: 1990
      harmonic: 3035
  Sorted by residual:
  dihedral pdb=" CA  TYR A1083 "
           pdb=" C   TYR A1083 "
           pdb=" N   PRO A1084 "
           pdb=" CA  PRO A1084 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.90   25.10     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  VAL A 252 "
           pdb=" C   VAL A 252 "
           pdb=" N   PHE A 253 "
           pdb=" CA  PHE A 253 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.79  -24.21     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  LEU A 754 "
           pdb=" C   LEU A 754 "
           pdb=" N   GLY A 755 "
           pdb=" CA  GLY A 755 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.18   22.82     0      5.00e+00 4.00e-02 2.08e+01
  ... (remaining 5022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1234
       0.074 -    0.149: 123
       0.149 -    0.223: 9
       0.223 -    0.297: 1
       0.297 -    0.371: 1
  Chirality restraints: 1368
  Sorted by residual:
  chirality pdb=" CB  ILE A 742 "
            pdb=" CA  ILE A 742 "
            pdb=" CG1 ILE A 742 "
            pdb=" CG2 ILE A 742 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.37 2.00e-01 2.50e+01 3.45e+00
  chirality pdb=" CB  VAL A 558 "
            pdb=" CA  VAL A 558 "
            pdb=" CG1 VAL A 558 "
            pdb=" CG2 VAL A 558 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  THR A1100 "
            pdb=" N   THR A1100 "
            pdb=" C   THR A1100 "
            pdb=" CB  THR A1100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1365 not shown)

  Planarity restraints: 1404
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 766 "    0.021 2.00e-02 2.50e+03   1.89e-02 6.28e+00
        pdb=" CG  PHE A 766 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 766 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 766 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 766 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 766 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 766 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 467 "    0.011 2.00e-02 2.50e+03   2.30e-02 5.27e+00
        pdb=" C   LEU A 467 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   LEU A 467 "    0.015 2.00e-02 2.50e+03
        pdb=" N   VAL A 468 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 275 "    0.032 5.00e-02 4.00e+02   4.87e-02 3.79e+00
        pdb=" N   PRO A 276 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 276 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 276 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1401 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1903
        2.79 -     3.32: 7688
        3.32 -     3.85: 13772
        3.85 -     4.37: 14686
        4.37 -     4.90: 27042
  Nonbonded interactions: 65091
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 469 "
            pdb=" OG1 THR A 473 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   ALA A 307 "
            pdb=" OG1 THR A 311 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   SER A 404 "
            pdb=" OG  SER A 407 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   SER A 407 "
            pdb=" OG  SER A 411 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" O   THR A1081 "
            pdb=" OG1 THR A1081 "
     model   vdw
     2.374 3.040
  ... (remaining 65086 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:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.430
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
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   0.060   8395  Z= 0.206
  Angle     :  0.737  11.669  11384  Z= 0.406
  Chirality :  0.046   0.371   1368
  Planarity :  0.006   0.049   1404
  Dihedral  : 12.524  80.482   3057
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  :  9.69 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.41 (0.23), residues: 1032
  helix: -0.58 (0.16), residues: 765
  sheet: -0.23 (0.76), residues: 46
  loop : -1.82 (0.38), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 635 
 HIS   0.002   0.000   HIS A 350 
 PHE   0.043   0.001   PHE A 766 
 TYR   0.010   0.001   TYR A 191 
 ARG   0.001   0.000   ARG A 887 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 307
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 VAL cc_start: 0.8064 (p) cc_final: 0.7749 (m)
REVERT: A  112 ILE cc_start: 0.8296 (mm) cc_final: 0.8062 (mm)
REVERT: A  135 PRO cc_start: 0.7864 (Cg_exo) cc_final: 0.7648 (Cg_endo)
REVERT: A  149 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7512 (tm-30)
REVERT: A  154 MET cc_start: 0.8483 (tpp) cc_final: 0.7751 (tpp)
REVERT: A  155 ASP cc_start: 0.8030 (t0) cc_final: 0.7797 (t0)
REVERT: A  158 THR cc_start: 0.8785 (p) cc_final: 0.8237 (p)
REVERT: A  163 PHE cc_start: 0.7856 (t80) cc_final: 0.7565 (t80)
REVERT: A  174 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8235 (tp)
REVERT: A  195 PHE cc_start: 0.7683 (t80) cc_final: 0.7394 (t80)
REVERT: A  197 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7803 (mt-10)
REVERT: A  231 GLU cc_start: 0.7618 (tt0) cc_final: 0.7280 (tt0)
REVERT: A  233 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7788 (tm-30)
REVERT: A  237 ASN cc_start: 0.8043 (t0) cc_final: 0.7835 (t0)
REVERT: A  246 ASN cc_start: 0.8281 (m-40) cc_final: 0.7997 (m110)
REVERT: A  249 MET cc_start: 0.8270 (tmm) cc_final: 0.7968 (ttp)
REVERT: A  284 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8355 (mmmm)
REVERT: A  338 LYS cc_start: 0.8590 (mtmm) cc_final: 0.8348 (mtmm)
REVERT: A  354 GLU cc_start: 0.8030 (tt0) cc_final: 0.7828 (tt0)
REVERT: A  363 LEU cc_start: 0.8460 (mt) cc_final: 0.7909 (mm)
REVERT: A  366 MET cc_start: 0.8353 (mmm) cc_final: 0.8089 (mmm)
REVERT: A  373 THR cc_start: 0.8538 (t) cc_final: 0.8326 (t)
REVERT: A  375 LYS cc_start: 0.8360 (ttpt) cc_final: 0.7957 (ttmm)
REVERT: A  386 PHE cc_start: 0.8088 (t80) cc_final: 0.7529 (t80)
REVERT: A  491 ARG cc_start: 0.8577 (tpp80) cc_final: 0.8261 (ttm-80)
REVERT: A  513 LYS cc_start: 0.8851 (mttt) cc_final: 0.8494 (mttm)
REVERT: A  531 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6953 (tm-30)
REVERT: A  588 LYS cc_start: 0.8316 (tppt) cc_final: 0.7896 (tppt)
REVERT: A  591 LYS cc_start: 0.8419 (mttt) cc_final: 0.7696 (mttt)
REVERT: A  609 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7697 (mmm-85)
REVERT: A  616 GLU cc_start: 0.7355 (pt0) cc_final: 0.7092 (pt0)
REVERT: A  621 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7334 (mp0)
REVERT: A  633 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8483 (mmtt)
REVERT: A  671 MET cc_start: 0.5881 (mmt) cc_final: 0.5272 (mmt)
REVERT: A  678 MET cc_start: 0.6303 (ppp) cc_final: 0.6045 (ppp)
REVERT: A  694 PRO cc_start: 0.7797 (Cg_exo) cc_final: 0.7482 (Cg_endo)
REVERT: A  697 MET cc_start: 0.7028 (mmm) cc_final: 0.6519 (mmm)
REVERT: A  800 LYS cc_start: 0.6928 (ttpp) cc_final: 0.6563 (tttp)
REVERT: A  824 VAL cc_start: 0.8640 (t) cc_final: 0.8415 (t)
REVERT: A  825 VAL cc_start: 0.8790 (t) cc_final: 0.8464 (p)
REVERT: A  832 GLN cc_start: 0.8384 (tp40) cc_final: 0.8131 (tt0)
REVERT: A  837 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8075 (t80)
REVERT: A  910 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7803 (ttm170)
REVERT: A  923 ASP cc_start: 0.7873 (p0) cc_final: 0.7601 (p0)
REVERT: A  926 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7110 (mm-30)
REVERT: A  935 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7967 (mt-10)
REVERT: A  981 HIS cc_start: 0.7990 (m90) cc_final: 0.7641 (m-70)
REVERT: A  993 ASP cc_start: 0.7338 (p0) cc_final: 0.7137 (p0)
REVERT: A  994 GLU cc_start: 0.8318 (pm20) cc_final: 0.7847 (pm20)
REVERT: A 1007 LYS cc_start: 0.8456 (tttp) cc_final: 0.8251 (ttmm)
REVERT: A 1044 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7437 (mt-10)
REVERT: A 1045 MET cc_start: 0.8206 (ttp) cc_final: 0.7950 (ttm)
REVERT: A 1066 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7830 (m-80)
REVERT: A 1075 ILE cc_start: 0.8269 (mm) cc_final: 0.8044 (mm)
REVERT: A 1087 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7514 (mm-30)
REVERT: A 1098 ILE cc_start: 0.8662 (tt) cc_final: 0.8458 (tt)
REVERT: A 1100 THR cc_start: 0.8629 (t) cc_final: 0.8215 (p)
REVERT: A 1110 GLN cc_start: 0.7386 (mp10) cc_final: 0.6888 (mp10)
REVERT: A 1122 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7364 (mm-30)
REVERT: A 1161 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7105 (pt)
REVERT: A 1190 ARG cc_start: 0.7388 (mpt180) cc_final: 0.6959 (mmt180)
  outliers start: 35
  outliers final: 9
  residues processed: 325
  average time/residue: 0.2576
  time to fit residues: 108.0043
Evaluate side-chains
  282 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 267
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  191 TYR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  443 GLU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  743 TYR
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  987 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1081 THR
Chi-restraints excluded: chain A residue 1161 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0670
   chunk 53 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
A 295 ASN
** A1114 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 = 0.3758 r_free = 0.3758 target = 0.136677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.118057 restraints weight = 12599.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.05
r_work: 0.3369 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8395  Z= 0.218
  Angle     :  0.577  14.305  11384  Z= 0.298
  Chirality :  0.040   0.183   1368
  Planarity :  0.004   0.039   1404
  Dihedral  :  7.011  59.690   1144
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 15.37 %
    Favored  : 80.51 %
  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:  0.41 (0.26), residues: 1032
  helix:  0.86 (0.19), residues: 763
  sheet: -0.30 (0.72), residues: 48
  loop : -1.46 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A1112 
 HIS   0.003   0.001   HIS A 908 
 PHE   0.030   0.001   PHE A 766 
 TYR   0.009   0.001   TYR A 309 
 ARG   0.009   0.001   ARG A 733 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 271
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 VAL cc_start: 0.8303 (p) cc_final: 0.7994 (m)
REVERT: A  112 ILE cc_start: 0.8512 (mm) cc_final: 0.8278 (mm)
REVERT: A  149 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7329 (tm-30)
REVERT: A  154 MET cc_start: 0.8515 (tpp) cc_final: 0.6896 (tpp)
REVERT: A  155 ASP cc_start: 0.7995 (t0) cc_final: 0.7756 (t0)
REVERT: A  176 VAL cc_start: 0.8563 (p) cc_final: 0.8270 (t)
REVERT: A  190 ASN cc_start: 0.8222 (p0) cc_final: 0.7983 (p0)
REVERT: A  197 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7775 (mt-10)
REVERT: A  231 GLU cc_start: 0.7443 (tt0) cc_final: 0.6926 (tt0)
REVERT: A  233 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7658 (tm-30)
REVERT: A  246 ASN cc_start: 0.8182 (m-40) cc_final: 0.7883 (m110)
REVERT: A  338 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8294 (mtmm)
REVERT: A  363 LEU cc_start: 0.8450 (mt) cc_final: 0.8235 (mt)
REVERT: A  373 THR cc_start: 0.8499 (t) cc_final: 0.8299 (t)
REVERT: A  375 LYS cc_start: 0.8318 (ttpt) cc_final: 0.8086 (ttmm)
REVERT: A  377 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8305 (mp)
REVERT: A  386 PHE cc_start: 0.8112 (t80) cc_final: 0.7523 (t80)
REVERT: A  480 ILE cc_start: 0.7971 (mt) cc_final: 0.7688 (mt)
REVERT: A  486 ILE cc_start: 0.8479 (mp) cc_final: 0.8275 (mm)
REVERT: A  491 ARG cc_start: 0.8580 (tpp80) cc_final: 0.8300 (ttm-80)
REVERT: A  499 ARG cc_start: 0.8253 (mtp-110) cc_final: 0.7894 (ttp80)
REVERT: A  588 LYS cc_start: 0.8253 (tppt) cc_final: 0.7906 (tppt)
REVERT: A  598 PHE cc_start: 0.8800 (t80) cc_final: 0.8251 (t80)
REVERT: A  609 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7667 (mmm-85)
REVERT: A  613 GLN cc_start: 0.8082 (tt0) cc_final: 0.7875 (tm-30)
REVERT: A  616 GLU cc_start: 0.7563 (pt0) cc_final: 0.7270 (pt0)
REVERT: A  621 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7081 (mp0)
REVERT: A  633 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8443 (mmtt)
REVERT: A  644 LEU cc_start: 0.8518 (mt) cc_final: 0.8299 (mp)
REVERT: A  671 MET cc_start: 0.6249 (mmt) cc_final: 0.5657 (mmt)
REVERT: A  678 MET cc_start: 0.6608 (ppp) cc_final: 0.6300 (ppp)
REVERT: A  697 MET cc_start: 0.6978 (mmm) cc_final: 0.6273 (mmm)
REVERT: A  837 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.8199 (t80)
REVERT: A  868 LYS cc_start: 0.8323 (mtpp) cc_final: 0.8110 (mtpp)
REVERT: A  900 GLN cc_start: 0.8264 (mm-40) cc_final: 0.8039 (mm110)
REVERT: A  926 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7416 (mm-30)
REVERT: A  928 HIS cc_start: 0.7691 (t-90) cc_final: 0.7472 (t-170)
REVERT: A  981 HIS cc_start: 0.8026 (m90) cc_final: 0.7722 (m-70)
REVERT: A  993 ASP cc_start: 0.7381 (p0) cc_final: 0.7174 (p0)
REVERT: A 1033 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7603 (mt-10)
REVERT: A 1044 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7802 (mt-10)
REVERT: A 1066 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7689 (m-80)
REVERT: A 1075 ILE cc_start: 0.8342 (mm) cc_final: 0.8116 (mm)
REVERT: A 1087 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7775 (mm-30)
REVERT: A 1110 GLN cc_start: 0.7581 (mp10) cc_final: 0.7141 (mp-120)
REVERT: A 1122 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7514 (mm-30)
REVERT: A 1190 ARG cc_start: 0.7443 (tpt170) cc_final: 0.7086 (mmt180)
  outliers start: 37
  outliers final: 14
  residues processed: 293
  average time/residue: 0.2369
  time to fit residues: 90.5646
Evaluate side-chains
  273 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 255
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 TYR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  384 ASP
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain A residue  736 ASN
Chi-restraints excluded: chain A residue  743 TYR
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  987 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1141 THR
Chi-restraints excluded: chain A residue 1161 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0060
   chunk 33 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0020
   overall best weight:    0.4604

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

Flipped N/Q/H residues before XYZ refinement:
A1040 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.138206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.119667 restraints weight = 12564.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.00
r_work: 0.3390 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8395  Z= 0.185
  Angle     :  0.564  12.928  11384  Z= 0.291
  Chirality :  0.039   0.170   1368
  Planarity :  0.004   0.038   1404
  Dihedral  :  6.111  55.984   1132
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 18.82 %
    Favored  : 77.84 %
  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:  0.99 (0.26), residues: 1032
  helix:  1.30 (0.19), residues: 761
  sheet:  0.29 (0.81), residues: 38
  loop : -1.37 (0.39), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1112 
 HIS   0.002   0.000   HIS A 908 
 PHE   0.026   0.001   PHE A 766 
 TYR   0.008   0.001   TYR A 309 
 ARG   0.009   0.000   ARG A 573 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 256
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 VAL cc_start: 0.8218 (p) cc_final: 0.7926 (m)
REVERT: A  129 ASP cc_start: 0.5844 (OUTLIER) cc_final: 0.5599 (p0)
REVERT: A  149 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7392 (tm-30)
REVERT: A  154 MET cc_start: 0.8534 (tpp) cc_final: 0.7330 (tpp)
REVERT: A  155 ASP cc_start: 0.7971 (t0) cc_final: 0.7567 (t0)
REVERT: A  158 THR cc_start: 0.8784 (m) cc_final: 0.8170 (p)
REVERT: A  176 VAL cc_start: 0.8543 (p) cc_final: 0.8258 (t)
REVERT: A  190 ASN cc_start: 0.8191 (p0) cc_final: 0.7941 (p0)
REVERT: A  197 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7785 (mt-10)
REVERT: A  206 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.8188 (t)
REVERT: A  231 GLU cc_start: 0.7460 (tt0) cc_final: 0.6923 (tt0)
REVERT: A  233 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7629 (tm-30)
REVERT: A  246 ASN cc_start: 0.8282 (m-40) cc_final: 0.7927 (m110)
REVERT: A  338 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8338 (mtmm)
REVERT: A  373 THR cc_start: 0.8473 (t) cc_final: 0.8267 (t)
REVERT: A  386 PHE cc_start: 0.8055 (t80) cc_final: 0.7527 (t80)
REVERT: A  412 ARG cc_start: 0.6955 (mtm180) cc_final: 0.6606 (mtm-85)
REVERT: A  491 ARG cc_start: 0.8576 (tpp80) cc_final: 0.8282 (ttm-80)
REVERT: A  499 ARG cc_start: 0.8092 (mtp-110) cc_final: 0.7757 (ttp80)
REVERT: A  524 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7639 (m-30)
REVERT: A  573 ARG cc_start: 0.7206 (mmm160) cc_final: 0.6718 (mmm160)
REVERT: A  588 LYS cc_start: 0.8170 (tppt) cc_final: 0.7901 (tppt)
REVERT: A  598 PHE cc_start: 0.8761 (t80) cc_final: 0.8368 (t80)
REVERT: A  609 ARG cc_start: 0.7738 (mmm-85) cc_final: 0.7462 (mmm-85)
REVERT: A  616 GLU cc_start: 0.7535 (pt0) cc_final: 0.7243 (pt0)
REVERT: A  621 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7177 (mp0)
REVERT: A  633 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8438 (mmtt)
REVERT: A  678 MET cc_start: 0.6545 (ppp) cc_final: 0.6201 (ppp)
REVERT: A  685 ASN cc_start: 0.8630 (m-40) cc_final: 0.8122 (m-40)
REVERT: A  697 MET cc_start: 0.6774 (mmm) cc_final: 0.6562 (mmm)
REVERT: A  727 LYS cc_start: 0.8296 (mmmt) cc_final: 0.8032 (ptpp)
REVERT: A  756 ARG cc_start: 0.7533 (mmp-170) cc_final: 0.6355 (pmt170)
REVERT: A  824 VAL cc_start: 0.8650 (t) cc_final: 0.8300 (m)
REVERT: A  837 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.8125 (t80)
REVERT: A  868 LYS cc_start: 0.8290 (mtpp) cc_final: 0.8069 (mtpp)
REVERT: A  886 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7942 (tt0)
REVERT: A  900 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8089 (mm110)
REVERT: A  911 GLU cc_start: 0.8018 (tt0) cc_final: 0.7810 (mt-10)
REVERT: A  926 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7283 (mm-30)
REVERT: A  928 HIS cc_start: 0.7759 (t-90) cc_final: 0.7530 (t-170)
REVERT: A  981 HIS cc_start: 0.7956 (m90) cc_final: 0.7748 (m-70)
REVERT: A 1044 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7807 (mt-10)
REVERT: A 1066 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7721 (m-80)
REVERT: A 1107 MET cc_start: 0.8099 (ttm) cc_final: 0.7891 (ttp)
REVERT: A 1110 GLN cc_start: 0.7639 (mp10) cc_final: 0.7222 (mp-120)
REVERT: A 1122 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7554 (mm-30)
REVERT: A 1139 ASP cc_start: 0.7528 (m-30) cc_final: 0.7267 (m-30)
REVERT: A 1190 ARG cc_start: 0.7415 (tpt170) cc_final: 0.7120 (mmt180)
  outliers start: 30
  outliers final: 16
  residues processed: 274
  average time/residue: 0.2339
  time to fit residues: 84.3581
Evaluate side-chains
  270 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 248
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ASP
Chi-restraints excluded: chain A residue  191 TYR
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  736 ASN
Chi-restraints excluded: chain A residue  743 TYR
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  987 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1115 GLU
Chi-restraints excluded: chain A residue 1161 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 86 optimal weight:    0.0040
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
A 126 HIS
A1040 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.137727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.119451 restraints weight = 12423.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 1.97
r_work: 0.3387 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8395  Z= 0.197
  Angle     :  0.567  13.795  11384  Z= 0.289
  Chirality :  0.039   0.167   1368
  Planarity :  0.004   0.034   1404
  Dihedral  :  6.070  59.508   1132
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 19.38 %
    Favored  : 76.61 %
  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:  1.18 (0.27), residues: 1032
  helix:  1.44 (0.19), residues: 761
  sheet:  0.54 (0.81), residues: 38
  loop : -1.30 (0.40), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 353 
 HIS   0.003   0.000   HIS A 908 
 PHE   0.026   0.001   PHE A 766 
 TYR   0.008   0.001   TYR A 309 
 ARG   0.005   0.000   ARG A 733 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 251
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 VAL cc_start: 0.8263 (p) cc_final: 0.7970 (m)
REVERT: A  120 VAL cc_start: 0.7701 (t) cc_final: 0.7403 (m)
REVERT: A  149 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7363 (tm-30)
REVERT: A  154 MET cc_start: 0.8483 (tpp) cc_final: 0.7203 (tpp)
REVERT: A  155 ASP cc_start: 0.7980 (t0) cc_final: 0.7680 (t0)
REVERT: A  176 VAL cc_start: 0.8520 (p) cc_final: 0.8246 (t)
REVERT: A  190 ASN cc_start: 0.8241 (p0) cc_final: 0.8011 (p0)
REVERT: A  197 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7814 (mt-10)
REVERT: A  206 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8153 (t)
REVERT: A  231 GLU cc_start: 0.7447 (tt0) cc_final: 0.6947 (tt0)
REVERT: A  233 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: A  246 ASN cc_start: 0.8289 (m-40) cc_final: 0.7951 (m110)
REVERT: A  277 LEU cc_start: 0.8543 (mm) cc_final: 0.8303 (mp)
REVERT: A  377 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8303 (mp)
REVERT: A  386 PHE cc_start: 0.8026 (t80) cc_final: 0.7576 (t80)
REVERT: A  491 ARG cc_start: 0.8545 (tpp80) cc_final: 0.8317 (ttm-80)
REVERT: A  524 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7615 (m-30)
REVERT: A  573 ARG cc_start: 0.7289 (mmm160) cc_final: 0.6634 (mmm160)
REVERT: A  588 LYS cc_start: 0.8143 (tppt) cc_final: 0.7869 (tppt)
REVERT: A  598 PHE cc_start: 0.8748 (t80) cc_final: 0.8347 (t80)
REVERT: A  609 ARG cc_start: 0.7691 (mmm-85) cc_final: 0.7429 (mmm-85)
REVERT: A  616 GLU cc_start: 0.7543 (pt0) cc_final: 0.7255 (pt0)
REVERT: A  621 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7175 (mp0)
REVERT: A  633 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8418 (mmtt)
REVERT: A  637 ILE cc_start: 0.8380 (tp) cc_final: 0.8113 (tp)
REVERT: A  678 MET cc_start: 0.6541 (ppp) cc_final: 0.6173 (ppp)
REVERT: A  685 ASN cc_start: 0.8609 (m-40) cc_final: 0.8208 (m-40)
REVERT: A  697 MET cc_start: 0.6848 (mmm) cc_final: 0.6527 (mmm)
REVERT: A  727 LYS cc_start: 0.8279 (mmmt) cc_final: 0.8076 (ptpp)
REVERT: A  824 VAL cc_start: 0.8646 (t) cc_final: 0.8283 (m)
REVERT: A  831 ASN cc_start: 0.8001 (m-40) cc_final: 0.7775 (m110)
REVERT: A  837 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.8200 (t80)
REVERT: A  926 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7343 (mm-30)
REVERT: A  940 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7778 (mtt90)
REVERT: A  981 HIS cc_start: 0.7933 (m90) cc_final: 0.7618 (m90)
REVERT: A  994 GLU cc_start: 0.8191 (pm20) cc_final: 0.7866 (pm20)
REVERT: A  999 PHE cc_start: 0.7608 (m-10) cc_final: 0.7366 (m-10)
REVERT: A 1044 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7732 (mt-10)
REVERT: A 1066 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7665 (m-80)
REVERT: A 1110 GLN cc_start: 0.7720 (mp10) cc_final: 0.7269 (mp-120)
REVERT: A 1122 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7550 (mm-30)
REVERT: A 1190 ARG cc_start: 0.7341 (tpt170) cc_final: 0.7054 (mmt180)
  outliers start: 36
  outliers final: 18
  residues processed: 269
  average time/residue: 0.2458
  time to fit residues: 86.5189
Evaluate side-chains
  267 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 243
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  191 TYR
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  736 ASN
Chi-restraints excluded: chain A residue  743 TYR
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  987 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1115 GLU
Chi-restraints excluded: chain A residue 1141 THR
Chi-restraints excluded: chain A residue 1161 ILE
Chi-restraints excluded: chain A residue 1179 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 48 optimal weight:   20.0000
   chunk 98 optimal weight:    0.3980
   chunk 5 optimal weight:    0.1980
   chunk 73 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 764 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.136644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.117836 restraints weight = 12314.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 2.10
r_work: 0.3361 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8395  Z= 0.221
  Angle     :  0.584  14.171  11384  Z= 0.296
  Chirality :  0.040   0.181   1368
  Planarity :  0.004   0.033   1404
  Dihedral  :  5.996  55.556   1132
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 20.38 %
    Favored  : 75.84 %
  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:  1.24 (0.26), residues: 1032
  helix:  1.47 (0.19), residues: 767
  sheet:  0.45 (0.79), residues: 38
  loop : -1.28 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 353 
 HIS   0.004   0.001   HIS A 908 
 PHE   0.027   0.001   PHE A 766 
 TYR   0.011   0.001   TYR A1153 
 ARG   0.008   0.000   ARG A 756 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 257
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 PHE cc_start: 0.8390 (m-10) cc_final: 0.8188 (m-10)
REVERT: A  105 VAL cc_start: 0.8227 (p) cc_final: 0.7940 (m)
REVERT: A  120 VAL cc_start: 0.7669 (t) cc_final: 0.7342 (m)
REVERT: A  149 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7323 (tm-30)
REVERT: A  154 MET cc_start: 0.8455 (tpp) cc_final: 0.7571 (tpp)
REVERT: A  155 ASP cc_start: 0.8109 (t0) cc_final: 0.7736 (t0)
REVERT: A  176 VAL cc_start: 0.8492 (p) cc_final: 0.8254 (t)
REVERT: A  190 ASN cc_start: 0.8251 (p0) cc_final: 0.7995 (p0)
REVERT: A  197 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7838 (mt-10)
REVERT: A  206 SER cc_start: 0.8564 (m) cc_final: 0.8093 (t)
REVERT: A  231 GLU cc_start: 0.7566 (tt0) cc_final: 0.7299 (tt0)
REVERT: A  233 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7601 (tm-30)
REVERT: A  246 ASN cc_start: 0.8272 (m-40) cc_final: 0.7914 (m110)
REVERT: A  277 LEU cc_start: 0.8546 (mm) cc_final: 0.8294 (mp)
REVERT: A  338 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8426 (mtmm)
REVERT: A  386 PHE cc_start: 0.8015 (t80) cc_final: 0.7528 (t80)
REVERT: A  465 LEU cc_start: 0.8419 (mt) cc_final: 0.8169 (mp)
REVERT: A  477 LEU cc_start: 0.8535 (tp) cc_final: 0.8223 (tp)
REVERT: A  491 ARG cc_start: 0.8493 (tpp80) cc_final: 0.8271 (ttm-80)
REVERT: A  499 ARG cc_start: 0.8077 (mtp-110) cc_final: 0.7833 (ttp80)
REVERT: A  516 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.8053 (ttt90)
REVERT: A  524 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7640 (m-30)
REVERT: A  573 ARG cc_start: 0.7330 (mmm160) cc_final: 0.6570 (mmm160)
REVERT: A  588 LYS cc_start: 0.8173 (tppt) cc_final: 0.7851 (tppt)
REVERT: A  598 PHE cc_start: 0.8702 (t80) cc_final: 0.8152 (t80)
REVERT: A  606 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7541 (pm20)
REVERT: A  609 ARG cc_start: 0.7805 (mmm-85) cc_final: 0.7491 (mmm-85)
REVERT: A  616 GLU cc_start: 0.7611 (pt0) cc_final: 0.7325 (pt0)
REVERT: A  621 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7261 (mp0)
REVERT: A  633 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8397 (mmtt)
REVERT: A  637 ILE cc_start: 0.8492 (tp) cc_final: 0.8191 (tp)
REVERT: A  678 MET cc_start: 0.6643 (ppp) cc_final: 0.6250 (ppp)
REVERT: A  685 ASN cc_start: 0.8624 (m-40) cc_final: 0.8185 (m-40)
REVERT: A  697 MET cc_start: 0.6359 (mmm) cc_final: 0.6156 (mmm)
REVERT: A  824 VAL cc_start: 0.8611 (t) cc_final: 0.8253 (m)
REVERT: A  831 ASN cc_start: 0.8141 (m-40) cc_final: 0.7895 (m110)
REVERT: A  837 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8146 (t80)
REVERT: A  868 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7946 (mtpp)
REVERT: A  876 LEU cc_start: 0.8484 (mt) cc_final: 0.8138 (mp)
REVERT: A  911 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7621 (mt-10)
REVERT: A  926 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7299 (mm-30)
REVERT: A  940 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7915 (mtt90)
REVERT: A  976 ARG cc_start: 0.8078 (mpt90) cc_final: 0.7801 (mpt180)
REVERT: A  981 HIS cc_start: 0.8051 (m90) cc_final: 0.7847 (m-70)
REVERT: A  994 GLU cc_start: 0.8272 (pm20) cc_final: 0.7959 (pm20)
REVERT: A 1044 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7831 (mt-10)
REVERT: A 1066 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7740 (m-80)
REVERT: A 1072 ASP cc_start: 0.7839 (m-30) cc_final: 0.7615 (m-30)
REVERT: A 1110 GLN cc_start: 0.7684 (mp10) cc_final: 0.7208 (mp-120)
REVERT: A 1115 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7563 (tp30)
REVERT: A 1122 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7502 (mm-30)
REVERT: A 1190 ARG cc_start: 0.7289 (tpt170) cc_final: 0.6987 (mmt180)
  outliers start: 34
  outliers final: 21
  residues processed: 275
  average time/residue: 0.2344
  time to fit residues: 84.3158
Evaluate side-chains
  279 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 252
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  191 TYR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  443 GLU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  736 ASN
Chi-restraints excluded: chain A residue  743 TYR
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  987 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1115 GLU
Chi-restraints excluded: chain A residue 1141 THR
Chi-restraints excluded: chain A residue 1179 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 81 optimal weight:    0.4980
   chunk 45 optimal weight:    0.0670
   chunk 2 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 76 optimal weight:    0.4980
   chunk 82 optimal weight:    1.9990
   chunk 57 optimal weight:    0.3980
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
** A 292 HIS ** 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 = 0.3762 r_free = 0.3762 target = 0.138085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.119928 restraints weight = 12395.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.97
r_work: 0.3395 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8395  Z= 0.177
  Angle     :  0.574  13.904  11384  Z= 0.293
  Chirality :  0.039   0.169   1368
  Planarity :  0.004   0.033   1404
  Dihedral  :  5.629  56.171   1130
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 21.16 %
    Favored  : 75.17 %
  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:  1.42 (0.27), residues: 1032
  helix:  1.59 (0.19), residues: 766
  sheet:  0.74 (0.80), residues: 38
  loop : -1.23 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 763 
 HIS   0.003   0.000   HIS A 757 
 PHE   0.024   0.001   PHE A 766 
 TYR   0.008   0.001   TYR A1153 
 ARG   0.005   0.000   ARG A1162 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 251
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 VAL cc_start: 0.8188 (p) cc_final: 0.7886 (m)
REVERT: A  120 VAL cc_start: 0.7712 (t) cc_final: 0.7408 (m)
REVERT: A  149 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7343 (tm-30)
REVERT: A  154 MET cc_start: 0.8431 (tpp) cc_final: 0.7547 (tpp)
REVERT: A  155 ASP cc_start: 0.8018 (t0) cc_final: 0.7680 (t0)
REVERT: A  176 VAL cc_start: 0.8511 (p) cc_final: 0.8250 (t)
REVERT: A  190 ASN cc_start: 0.8254 (p0) cc_final: 0.8008 (p0)
REVERT: A  197 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7842 (mt-10)
REVERT: A  206 SER cc_start: 0.8605 (m) cc_final: 0.8171 (t)
REVERT: A  217 LEU cc_start: 0.8708 (mt) cc_final: 0.8308 (mp)
REVERT: A  231 GLU cc_start: 0.7503 (tt0) cc_final: 0.7280 (tt0)
REVERT: A  233 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7620 (tm-30)
REVERT: A  246 ASN cc_start: 0.8258 (m-40) cc_final: 0.7925 (m110)
REVERT: A  286 THR cc_start: 0.8619 (m) cc_final: 0.8349 (p)
REVERT: A  386 PHE cc_start: 0.7986 (t80) cc_final: 0.7542 (t80)
REVERT: A  412 ARG cc_start: 0.7193 (mtm180) cc_final: 0.6949 (mtm180)
REVERT: A  465 LEU cc_start: 0.8443 (mt) cc_final: 0.8197 (mp)
REVERT: A  477 LEU cc_start: 0.8464 (tp) cc_final: 0.8159 (tp)
REVERT: A  491 ARG cc_start: 0.8517 (tpp80) cc_final: 0.8279 (ttm-80)
REVERT: A  499 ARG cc_start: 0.8030 (mtp-110) cc_final: 0.7788 (ttp80)
REVERT: A  516 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.8089 (ttt90)
REVERT: A  524 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7601 (m-30)
REVERT: A  573 ARG cc_start: 0.7325 (mmm160) cc_final: 0.6586 (mmm160)
REVERT: A  588 LYS cc_start: 0.8111 (tppt) cc_final: 0.7837 (tppt)
REVERT: A  598 PHE cc_start: 0.8683 (t80) cc_final: 0.8149 (t80)
REVERT: A  606 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7596 (pm20)
REVERT: A  609 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7423 (mmm-85)
REVERT: A  616 GLU cc_start: 0.7546 (pt0) cc_final: 0.7259 (pt0)
REVERT: A  621 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7312 (mp0)
REVERT: A  633 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8371 (mmtt)
REVERT: A  637 ILE cc_start: 0.8427 (tp) cc_final: 0.8168 (tp)
REVERT: A  678 MET cc_start: 0.6553 (ppp) cc_final: 0.6164 (ppp)
REVERT: A  685 ASN cc_start: 0.8555 (m-40) cc_final: 0.8146 (m-40)
REVERT: A  697 MET cc_start: 0.6245 (mmm) cc_final: 0.6037 (mmm)
REVERT: A  756 ARG cc_start: 0.7357 (mmp80) cc_final: 0.6331 (ppt170)
REVERT: A  824 VAL cc_start: 0.8629 (t) cc_final: 0.8259 (m)
REVERT: A  831 ASN cc_start: 0.8005 (m-40) cc_final: 0.7753 (m110)
REVERT: A  837 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8157 (t80)
REVERT: A  868 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7974 (mtpp)
REVERT: A  876 LEU cc_start: 0.8478 (mt) cc_final: 0.8127 (mp)
REVERT: A  911 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7660 (mt-10)
REVERT: A  926 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7299 (mm-30)
REVERT: A  940 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7772 (mtt90)
REVERT: A  981 HIS cc_start: 0.7933 (m90) cc_final: 0.7609 (m90)
REVERT: A  994 GLU cc_start: 0.8200 (pm20) cc_final: 0.7932 (pm20)
REVERT: A 1007 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8338 (ttmt)
REVERT: A 1044 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7654 (mt-10)
REVERT: A 1066 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7681 (m-80)
REVERT: A 1104 MET cc_start: 0.7863 (tmm) cc_final: 0.7649 (tmm)
REVERT: A 1105 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8128 (tm-30)
REVERT: A 1110 GLN cc_start: 0.7763 (mp10) cc_final: 0.7327 (mp-120)
REVERT: A 1115 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7604 (tp30)
REVERT: A 1122 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7530 (mm-30)
REVERT: A 1160 GLU cc_start: 0.7290 (tp30) cc_final: 0.6933 (tp30)
REVERT: A 1190 ARG cc_start: 0.7295 (tpt170) cc_final: 0.7027 (mmt180)
  outliers start: 33
  outliers final: 23
  residues processed: 269
  average time/residue: 0.2444
  time to fit residues: 86.6357
Evaluate side-chains
  276 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 247
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  191 TYR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  443 GLU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  736 ASN
Chi-restraints excluded: chain A residue  743 TYR
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  987 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1068 ILE
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1114 GLN
Chi-restraints excluded: chain A residue 1115 GLU
Chi-restraints excluded: chain A residue 1141 THR
Chi-restraints excluded: chain A residue 1179 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 98 optimal weight:    0.6980
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.136491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.118470 restraints weight = 12344.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.97
r_work: 0.3377 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8395  Z= 0.243
  Angle     :  0.596  14.522  11384  Z= 0.304
  Chirality :  0.041   0.171   1368
  Planarity :  0.004   0.032   1404
  Dihedral  :  5.727  57.198   1130
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 22.16 %
    Favored  : 74.05 %
  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:  1.38 (0.26), residues: 1032
  helix:  1.56 (0.19), residues: 767
  sheet:  0.77 (0.80), residues: 38
  loop : -1.27 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 353 
 HIS   0.004   0.000   HIS A 908 
 PHE   0.026   0.002   PHE A 766 
 TYR   0.011   0.001   TYR A 309 
 ARG   0.005   0.000   ARG A1162 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 253
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 VAL cc_start: 0.8258 (p) cc_final: 0.7948 (m)
REVERT: A  120 VAL cc_start: 0.7771 (t) cc_final: 0.7477 (m)
REVERT: A  149 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7327 (tm-30)
REVERT: A  154 MET cc_start: 0.8480 (tpp) cc_final: 0.7642 (tpp)
REVERT: A  155 ASP cc_start: 0.8011 (t0) cc_final: 0.7764 (t0)
REVERT: A  176 VAL cc_start: 0.8548 (p) cc_final: 0.8317 (t)
REVERT: A  190 ASN cc_start: 0.8274 (p0) cc_final: 0.8029 (p0)
REVERT: A  197 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7886 (mt-10)
REVERT: A  206 SER cc_start: 0.8610 (m) cc_final: 0.8170 (t)
REVERT: A  231 GLU cc_start: 0.7507 (tt0) cc_final: 0.7287 (tt0)
REVERT: A  233 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7589 (tm-30)
REVERT: A  277 LEU cc_start: 0.8533 (mm) cc_final: 0.8301 (mp)
REVERT: A  386 PHE cc_start: 0.7982 (t80) cc_final: 0.7522 (t80)
REVERT: A  412 ARG cc_start: 0.7214 (mtm180) cc_final: 0.6926 (mtm180)
REVERT: A  465 LEU cc_start: 0.8453 (mt) cc_final: 0.8201 (mp)
REVERT: A  491 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8299 (ttm-80)
REVERT: A  499 ARG cc_start: 0.8012 (mtp-110) cc_final: 0.7761 (ttp80)
REVERT: A  516 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.8045 (ttt90)
REVERT: A  524 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7607 (m-30)
REVERT: A  573 ARG cc_start: 0.7353 (mmm160) cc_final: 0.6592 (mmm160)
REVERT: A  588 LYS cc_start: 0.8114 (tppt) cc_final: 0.7853 (tppt)
REVERT: A  598 PHE cc_start: 0.8691 (t80) cc_final: 0.8209 (t80)
REVERT: A  606 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7604 (pm20)
REVERT: A  609 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.7416 (mmm-85)
REVERT: A  616 GLU cc_start: 0.7548 (pt0) cc_final: 0.7268 (pt0)
REVERT: A  621 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7380 (mp0)
REVERT: A  633 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8378 (mmtt)
REVERT: A  637 ILE cc_start: 0.8522 (tp) cc_final: 0.8239 (tp)
REVERT: A  678 MET cc_start: 0.6587 (ppp) cc_final: 0.6203 (ppp)
REVERT: A  685 ASN cc_start: 0.8544 (m-40) cc_final: 0.8155 (m-40)
REVERT: A  697 MET cc_start: 0.6408 (mmm) cc_final: 0.6190 (mmm)
REVERT: A  756 ARG cc_start: 0.7367 (mmp80) cc_final: 0.6450 (ptt-90)
REVERT: A  824 VAL cc_start: 0.8616 (t) cc_final: 0.8259 (m)
REVERT: A  831 ASN cc_start: 0.8056 (m-40) cc_final: 0.7807 (m110)
REVERT: A  837 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8048 (t80)
REVERT: A  868 LYS cc_start: 0.8193 (mtpp) cc_final: 0.7933 (mtpp)
REVERT: A  876 LEU cc_start: 0.8441 (mt) cc_final: 0.8109 (mp)
REVERT: A  911 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7607 (mt-10)
REVERT: A  926 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7276 (mm-30)
REVERT: A  994 GLU cc_start: 0.8185 (pm20) cc_final: 0.7940 (pm20)
REVERT: A 1007 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8335 (ttmt)
REVERT: A 1044 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7682 (mt-10)
REVERT: A 1066 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7762 (m-80)
REVERT: A 1110 GLN cc_start: 0.7851 (mp10) cc_final: 0.7416 (mp-120)
REVERT: A 1115 GLU cc_start: 0.7815 (tp30) cc_final: 0.7545 (tp30)
REVERT: A 1122 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7529 (mm-30)
REVERT: A 1190 ARG cc_start: 0.7274 (tpt170) cc_final: 0.6983 (mmt180)
  outliers start: 34
  outliers final: 25
  residues processed: 273
  average time/residue: 0.2383
  time to fit residues: 85.1209
Evaluate side-chains
  279 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 248
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  191 TYR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  443 GLU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  736 ASN
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  872 GLU
Chi-restraints excluded: chain A residue  987 VAL
Chi-restraints excluded: chain A residue 1007 LYS
Chi-restraints excluded: chain A residue 1045 MET
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1068 ILE
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1141 THR
Chi-restraints excluded: chain A residue 1161 ILE
Chi-restraints excluded: chain A residue 1179 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 101 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.136809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.118642 restraints weight = 12405.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.99
r_work: 0.3379 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8395  Z= 0.229
  Angle     :  0.609  14.393  11384  Z= 0.311
  Chirality :  0.041   0.175   1368
  Planarity :  0.004   0.032   1404
  Dihedral  :  5.528  57.690   1128
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 22.38 %
    Favored  : 73.50 %
  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:  1.43 (0.27), residues: 1032
  helix:  1.61 (0.19), residues: 767
  sheet:  0.83 (0.80), residues: 38
  loop : -1.27 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 353 
 HIS   0.004   0.000   HIS A 908 
 PHE   0.027   0.002   PHE A 766 
 TYR   0.013   0.001   TYR A 387 
 ARG   0.006   0.000   ARG A1162 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 254
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 VAL cc_start: 0.8235 (p) cc_final: 0.7940 (m)
REVERT: A  120 VAL cc_start: 0.7750 (t) cc_final: 0.7455 (m)
REVERT: A  149 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7319 (tm-30)
REVERT: A  154 MET cc_start: 0.8465 (tpp) cc_final: 0.7656 (tpp)
REVERT: A  155 ASP cc_start: 0.8050 (t0) cc_final: 0.7498 (t0)
REVERT: A  176 VAL cc_start: 0.8543 (p) cc_final: 0.8304 (t)
REVERT: A  206 SER cc_start: 0.8634 (m) cc_final: 0.8155 (t)
REVERT: A  217 LEU cc_start: 0.8685 (mt) cc_final: 0.8285 (mp)
REVERT: A  231 GLU cc_start: 0.7518 (tt0) cc_final: 0.7279 (tt0)
REVERT: A  233 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7575 (tm-30)
REVERT: A  277 LEU cc_start: 0.8543 (mm) cc_final: 0.8303 (mp)
REVERT: A  383 MET cc_start: 0.6960 (mmm) cc_final: 0.6584 (mmm)
REVERT: A  386 PHE cc_start: 0.7984 (t80) cc_final: 0.7520 (t80)
REVERT: A  387 TYR cc_start: 0.8297 (m-10) cc_final: 0.7842 (m-10)
REVERT: A  412 ARG cc_start: 0.7271 (mtm180) cc_final: 0.6960 (mtm180)
REVERT: A  465 LEU cc_start: 0.8440 (mt) cc_final: 0.8192 (mp)
REVERT: A  477 LEU cc_start: 0.8555 (tp) cc_final: 0.8304 (tp)
REVERT: A  491 ARG cc_start: 0.8530 (tpp80) cc_final: 0.8275 (ttm-80)
REVERT: A  516 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.8053 (ttt90)
REVERT: A  524 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7606 (m-30)
REVERT: A  573 ARG cc_start: 0.7353 (mmm160) cc_final: 0.6583 (mmm160)
REVERT: A  588 LYS cc_start: 0.8064 (tppt) cc_final: 0.7815 (tppt)
REVERT: A  598 PHE cc_start: 0.8685 (t80) cc_final: 0.8165 (t80)
REVERT: A  606 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7609 (pm20)
REVERT: A  609 ARG cc_start: 0.7714 (mmm-85) cc_final: 0.7444 (mmm-85)
REVERT: A  616 GLU cc_start: 0.7542 (pt0) cc_final: 0.7262 (pt0)
REVERT: A  621 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7414 (mp0)
REVERT: A  633 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8396 (mmtt)
REVERT: A  637 ILE cc_start: 0.8520 (tp) cc_final: 0.8226 (tp)
REVERT: A  678 MET cc_start: 0.6597 (ppp) cc_final: 0.6209 (ppp)
REVERT: A  685 ASN cc_start: 0.8536 (m-40) cc_final: 0.8236 (m-40)
REVERT: A  697 MET cc_start: 0.6386 (mmm) cc_final: 0.6107 (mmm)
REVERT: A  698 GLU cc_start: 0.7885 (pp20) cc_final: 0.7675 (tm-30)
REVERT: A  756 ARG cc_start: 0.7338 (mmp80) cc_final: 0.6489 (ptt-90)
REVERT: A  824 VAL cc_start: 0.8616 (t) cc_final: 0.8252 (m)
REVERT: A  831 ASN cc_start: 0.8074 (m-40) cc_final: 0.7813 (m110)
REVERT: A  835 LEU cc_start: 0.8634 (tt) cc_final: 0.8311 (tp)
REVERT: A  837 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8066 (t80)
REVERT: A  847 GLU cc_start: 0.8025 (tp30) cc_final: 0.7774 (tp30)
REVERT: A  876 LEU cc_start: 0.8426 (mt) cc_final: 0.8079 (mp)
REVERT: A  911 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7610 (mt-10)
REVERT: A  926 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7266 (mm-30)
REVERT: A  994 GLU cc_start: 0.8245 (pm20) cc_final: 0.8003 (pm20)
REVERT: A 1007 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8319 (ttmt)
REVERT: A 1044 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7629 (mt-10)
REVERT: A 1066 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7790 (m-80)
REVERT: A 1104 MET cc_start: 0.8185 (ttt) cc_final: 0.7896 (mtp)
REVERT: A 1110 GLN cc_start: 0.7887 (mp10) cc_final: 0.7392 (mp-120)
REVERT: A 1122 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7533 (mm-30)
REVERT: A 1190 ARG cc_start: 0.7250 (tpt170) cc_final: 0.7027 (mmt180)
  outliers start: 37
  outliers final: 26
  residues processed: 273
  average time/residue: 0.2264
  time to fit residues: 81.4594
Evaluate side-chains
  290 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 258
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  191 TYR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  443 GLU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  736 ASN
Chi-restraints excluded: chain A residue  743 TYR
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  872 GLU
Chi-restraints excluded: chain A residue  910 ARG
Chi-restraints excluded: chain A residue  987 VAL
Chi-restraints excluded: chain A residue 1007 LYS
Chi-restraints excluded: chain A residue 1045 MET
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1068 ILE
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1141 THR
Chi-restraints excluded: chain A residue 1161 ILE
Chi-restraints excluded: chain A residue 1179 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 93 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 66 optimal weight:    0.6980
   chunk 2 optimal weight:    0.4980
   chunk 27 optimal weight:    0.4980
   chunk 28 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 165 GLN
** A 691 ASN ** 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 = 0.3753 r_free = 0.3753 target = 0.137171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.119268 restraints weight = 12579.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 1.99
r_work: 0.3386 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8395  Z= 0.207
  Angle     :  0.617  14.381  11384  Z= 0.313
  Chirality :  0.041   0.187   1368
  Planarity :  0.004   0.033   1404
  Dihedral  :  5.387  58.303   1126
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 22.72 %
    Favored  : 73.27 %
  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:  1.48 (0.27), residues: 1032
  helix:  1.63 (0.19), residues: 767
  sheet:  0.87 (0.77), residues: 38
  loop : -1.20 (0.41), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1112 
 HIS   0.003   0.000   HIS A 908 
 PHE   0.027   0.001   PHE A 766 
 TYR   0.008   0.001   TYR A 309 
 ARG   0.007   0.000   ARG A 976 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 256
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 VAL cc_start: 0.8187 (p) cc_final: 0.7894 (m)
REVERT: A  120 VAL cc_start: 0.7736 (t) cc_final: 0.7448 (m)
REVERT: A  149 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7358 (tm-30)
REVERT: A  154 MET cc_start: 0.8482 (tpp) cc_final: 0.7642 (tpp)
REVERT: A  176 VAL cc_start: 0.8554 (p) cc_final: 0.8303 (t)
REVERT: A  206 SER cc_start: 0.8625 (m) cc_final: 0.8153 (t)
REVERT: A  217 LEU cc_start: 0.8680 (mt) cc_final: 0.8290 (mp)
REVERT: A  231 GLU cc_start: 0.7543 (tt0) cc_final: 0.7314 (tt0)
REVERT: A  233 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7551 (tm-30)
REVERT: A  277 LEU cc_start: 0.8545 (mm) cc_final: 0.8305 (mp)
REVERT: A  286 THR cc_start: 0.8605 (m) cc_final: 0.8338 (p)
REVERT: A  383 MET cc_start: 0.6890 (mmm) cc_final: 0.6559 (mmm)
REVERT: A  386 PHE cc_start: 0.7967 (t80) cc_final: 0.7516 (t80)
REVERT: A  387 TYR cc_start: 0.8262 (m-10) cc_final: 0.7865 (m-10)
REVERT: A  412 ARG cc_start: 0.7318 (mtm180) cc_final: 0.7030 (mtm180)
REVERT: A  477 LEU cc_start: 0.8502 (tp) cc_final: 0.8232 (tp)
REVERT: A  491 ARG cc_start: 0.8534 (tpp80) cc_final: 0.8270 (ttm-80)
REVERT: A  516 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7977 (ttt90)
REVERT: A  524 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7614 (m-30)
REVERT: A  573 ARG cc_start: 0.7331 (mmm160) cc_final: 0.6539 (mmm160)
REVERT: A  588 LYS cc_start: 0.8075 (tppt) cc_final: 0.7820 (tppt)
REVERT: A  598 PHE cc_start: 0.8689 (t80) cc_final: 0.8181 (t80)
REVERT: A  606 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7606 (pm20)
REVERT: A  609 ARG cc_start: 0.7674 (mmm-85) cc_final: 0.7390 (mmm-85)
REVERT: A  616 GLU cc_start: 0.7540 (pt0) cc_final: 0.7260 (pt0)
REVERT: A  621 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7423 (mp0)
REVERT: A  633 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8360 (mmtt)
REVERT: A  637 ILE cc_start: 0.8492 (tp) cc_final: 0.8226 (tp)
REVERT: A  671 MET cc_start: 0.6619 (mmt) cc_final: 0.6130 (mmt)
REVERT: A  678 MET cc_start: 0.6609 (ppp) cc_final: 0.6216 (ppp)
REVERT: A  685 ASN cc_start: 0.8489 (m-40) cc_final: 0.8201 (m-40)
REVERT: A  697 MET cc_start: 0.6274 (mmm) cc_final: 0.5959 (mmm)
REVERT: A  698 GLU cc_start: 0.7835 (pp20) cc_final: 0.7546 (tm-30)
REVERT: A  756 ARG cc_start: 0.7307 (mmp80) cc_final: 0.6464 (ptt-90)
REVERT: A  824 VAL cc_start: 0.8610 (t) cc_final: 0.8245 (m)
REVERT: A  831 ASN cc_start: 0.8026 (m-40) cc_final: 0.7766 (m110)
REVERT: A  835 LEU cc_start: 0.8622 (tt) cc_final: 0.8313 (tp)
REVERT: A  837 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8155 (t80)
REVERT: A  876 LEU cc_start: 0.8431 (mt) cc_final: 0.8100 (mp)
REVERT: A  881 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7927 (mt-10)
REVERT: A  911 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7620 (mt-10)
REVERT: A  926 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7269 (mm-30)
REVERT: A  994 GLU cc_start: 0.8193 (pm20) cc_final: 0.7974 (pm20)
REVERT: A 1007 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8264 (ttmm)
REVERT: A 1044 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7699 (mt-10)
REVERT: A 1066 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7731 (m-80)
REVERT: A 1105 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7952 (tm-30)
REVERT: A 1110 GLN cc_start: 0.7872 (mp10) cc_final: 0.7374 (mp-120)
REVERT: A 1122 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7561 (mm-30)
REVERT: A 1190 ARG cc_start: 0.7279 (tpt170) cc_final: 0.6945 (mmt180)
  outliers start: 36
  outliers final: 24
  residues processed: 275
  average time/residue: 0.2303
  time to fit residues: 83.2393
Evaluate side-chains
  277 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 247
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  191 TYR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  443 GLU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  736 ASN
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  872 GLU
Chi-restraints excluded: chain A residue  910 ARG
Chi-restraints excluded: chain A residue  987 VAL
Chi-restraints excluded: chain A residue 1007 LYS
Chi-restraints excluded: chain A residue 1045 MET
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1114 GLN
Chi-restraints excluded: chain A residue 1141 THR
Chi-restraints excluded: chain A residue 1161 ILE
Chi-restraints excluded: chain A residue 1179 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 103 optimal weight:    0.7980
   chunk 94 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   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 165 GLN
A 764 ASN
A 981 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.136602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.118786 restraints weight = 12351.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.96
r_work: 0.3381 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8395  Z= 0.241
  Angle     :  0.625  14.845  11384  Z= 0.319
  Chirality :  0.041   0.183   1368
  Planarity :  0.004   0.031   1404
  Dihedral  :  5.460  58.991   1126
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 23.39 %
    Favored  : 72.94 %
  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:  1.42 (0.26), residues: 1032
  helix:  1.59 (0.19), residues: 767
  sheet:  0.81 (0.78), residues: 38
  loop : -1.25 (0.41), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 353 
 HIS   0.004   0.000   HIS A 908 
 PHE   0.028   0.001   PHE A 999 
 TYR   0.010   0.001   TYR A 309 
 ARG   0.007   0.000   ARG A1162 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 250
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 VAL cc_start: 0.8225 (p) cc_final: 0.7927 (m)
REVERT: A  120 VAL cc_start: 0.7793 (t) cc_final: 0.7509 (m)
REVERT: A  149 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7330 (tm-30)
REVERT: A  154 MET cc_start: 0.8490 (tpp) cc_final: 0.7637 (tpp)
REVERT: A  176 VAL cc_start: 0.8561 (p) cc_final: 0.8315 (t)
REVERT: A  206 SER cc_start: 0.8632 (m) cc_final: 0.8148 (t)
REVERT: A  217 LEU cc_start: 0.8692 (mt) cc_final: 0.8292 (mp)
REVERT: A  231 GLU cc_start: 0.7507 (tt0) cc_final: 0.7292 (tt0)
REVERT: A  233 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7581 (tm-30)
REVERT: A  277 LEU cc_start: 0.8569 (mm) cc_final: 0.8320 (mp)
REVERT: A  303 ILE cc_start: 0.8567 (mp) cc_final: 0.8291 (mp)
REVERT: A  383 MET cc_start: 0.6891 (mmm) cc_final: 0.6541 (mmm)
REVERT: A  386 PHE cc_start: 0.7967 (t80) cc_final: 0.7514 (t80)
REVERT: A  387 TYR cc_start: 0.8314 (m-10) cc_final: 0.7899 (m-10)
REVERT: A  412 ARG cc_start: 0.7310 (mtm180) cc_final: 0.7010 (mtm180)
REVERT: A  477 LEU cc_start: 0.8542 (tp) cc_final: 0.8288 (tp)
REVERT: A  491 ARG cc_start: 0.8522 (tpp80) cc_final: 0.8265 (ttm-80)
REVERT: A  516 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.8012 (ttt90)
REVERT: A  524 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7623 (m-30)
REVERT: A  532 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7900 (mt)
REVERT: A  573 ARG cc_start: 0.7311 (mmm160) cc_final: 0.6522 (mmm160)
REVERT: A  588 LYS cc_start: 0.8057 (tppt) cc_final: 0.7811 (tppt)
REVERT: A  598 PHE cc_start: 0.8693 (t80) cc_final: 0.8191 (t80)
REVERT: A  606 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7617 (pm20)
REVERT: A  609 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.7348 (mmm-85)
REVERT: A  616 GLU cc_start: 0.7506 (pt0) cc_final: 0.7220 (pt0)
REVERT: A  621 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7412 (mp0)
REVERT: A  633 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8372 (mmtt)
REVERT: A  671 MET cc_start: 0.6649 (mmt) cc_final: 0.6203 (mmt)
REVERT: A  678 MET cc_start: 0.6650 (ppp) cc_final: 0.6254 (ppp)
REVERT: A  685 ASN cc_start: 0.8464 (m-40) cc_final: 0.8177 (m-40)
REVERT: A  697 MET cc_start: 0.6311 (mmm) cc_final: 0.6013 (mmm)
REVERT: A  698 GLU cc_start: 0.7854 (pp20) cc_final: 0.7571 (tm-30)
REVERT: A  756 ARG cc_start: 0.7318 (mmp80) cc_final: 0.6473 (ptt-90)
REVERT: A  824 VAL cc_start: 0.8610 (t) cc_final: 0.8257 (m)
REVERT: A  831 ASN cc_start: 0.8072 (m-40) cc_final: 0.7811 (m110)
REVERT: A  835 LEU cc_start: 0.8629 (tt) cc_final: 0.8327 (tp)
REVERT: A  837 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.8109 (t80)
REVERT: A  876 LEU cc_start: 0.8420 (mt) cc_final: 0.8082 (mp)
REVERT: A  900 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7964 (mm110)
REVERT: A  911 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7603 (mt-10)
REVERT: A  926 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7293 (mm-30)
REVERT: A  994 GLU cc_start: 0.8199 (pm20) cc_final: 0.7984 (pm20)
REVERT: A 1007 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8328 (ttmt)
REVERT: A 1044 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7705 (mt-10)
REVERT: A 1066 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7805 (m-80)
REVERT: A 1107 MET cc_start: 0.8234 (ttm) cc_final: 0.7670 (ptm)
REVERT: A 1110 GLN cc_start: 0.7867 (mp10) cc_final: 0.7405 (mp-120)
REVERT: A 1122 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7570 (mm-30)
REVERT: A 1190 ARG cc_start: 0.7264 (tpt170) cc_final: 0.6970 (mmt180)
  outliers start: 33
  outliers final: 24
  residues processed: 268
  average time/residue: 0.2403
  time to fit residues: 84.7619
Evaluate side-chains
  277 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 246
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  191 TYR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  443 GLU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  736 ASN
Chi-restraints excluded: chain A residue  743 TYR
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  822 ILE
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  872 GLU
Chi-restraints excluded: chain A residue  910 ARG
Chi-restraints excluded: chain A residue  915 GLU
Chi-restraints excluded: chain A residue  987 VAL
Chi-restraints excluded: chain A residue 1007 LYS
Chi-restraints excluded: chain A residue 1045 MET
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1100 THR
Chi-restraints excluded: chain A residue 1141 THR
Chi-restraints excluded: chain A residue 1179 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 76 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0870
   chunk 39 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0770
   overall best weight:    0.4116

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

Flipped N/Q/H residues before XYZ refinement:
A 764 ASN
A 981 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.137950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.120099 restraints weight = 12528.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.99
r_work: 0.3399 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8395  Z= 0.185
  Angle     :  0.621  14.270  11384  Z= 0.313
  Chirality :  0.040   0.195   1368
  Planarity :  0.004   0.032   1404
  Dihedral  :  5.388  59.571   1126
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 23.72 %
    Favored  : 72.38 %
  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:  1.51 (0.27), residues: 1032
  helix:  1.68 (0.19), residues: 761
  sheet:  0.84 (0.77), residues: 38
  loop : -1.21 (0.40), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1112 
 HIS   0.002   0.000   HIS A 908 
 PHE   0.029   0.001   PHE A 766 
 TYR   0.007   0.001   TYR A 309 
 ARG   0.007   0.000   ARG A1162 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4502.22 seconds
wall clock time: 80 minutes 16.74 seconds (4816.74 seconds total)