Starting phenix.real_space_refine
on Tue Jan 14 06:23:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y6k_38989/01_2025/8y6k_38989_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y6k_38989/01_2025/8y6k_38989.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y6k_38989/01_2025/8y6k_38989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y6k_38989/01_2025/8y6k_38989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y6k_38989/01_2025/8y6k_38989_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y6k_38989/01_2025/8y6k_38989_neut.cif"
  }
  resolution = 3.94
  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=   0.002 sd=   0.032
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P       2      5.49       5
     S      27      5.16       5
     C    3730      2.51       5
     N    1043      2.21       5
     O    1068      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 5872
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 741, 5817
          Classifications: {'peptide': 741}
          Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 708}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 55
          Unusual residues: {' ZN': 2, 'FAD': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4585  SG  CYS A2831      21.039  28.747  32.410  1.00155.18           S
  ATOM   4780  SG  CYS A2855      23.703  28.222  35.464  1.00173.43           S
  ATOM   4808  SG  CYS A2858      30.568  18.829  42.137  1.00172.10           S
  ATOM   4831  SG  CYS A2861      31.649  19.775  45.449  1.00184.76           S
  ATOM   4991  SG  CYS A2881      33.957  20.306  42.456  1.00177.40           S

  Time building chain proxies: 3.86, per 1000 atoms: 0.66
  Number of scatterers: 5872
  At special positions: 0
  Unit cell: (69.94, 81.776, 121.588, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      27     16.00
     P       2     15.00
     O    1068      8.00
     N    1043      7.00
     C    3730      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: 1.54
  Conformation dependent library (CDL) restraints added in 892.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A4301 "
        pdb="ZN    ZN A4301 " - pdb=" SG  CYS A2831 "
        pdb="ZN    ZN A4301 " - pdb=" SG  CYS A2855 "
      pdb="  ZN A4302 "
        pdb="ZN    ZN A4302 " - pdb=" ND1 HIS A2884 "
        pdb="ZN    ZN A4302 " - pdb=" SG  CYS A2861 "
        pdb="ZN    ZN A4302 " - pdb=" SG  CYS A2858 "
        pdb="ZN    ZN A4302 " - pdb=" SG  CYS A2881 "
      Number of angles added : 3


  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1364

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 6 sheets defined
      50.6% alpha, 9.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 19
    Processing helix  chain 'A' and resid 22 through 36
    Processing helix  chain 'A' and resid 45 through 52
      removed outlier: 4.083A  pdb=" N   HIS A  49 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LYS A  52 " --> pdb=" O   TYR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 59
      No H-bonds generated for 'chain 'A' and resid 57 through 59'
    Processing helix  chain 'A' and resid 60 through 72
    Processing helix  chain 'A' and resid 73 through 80
      removed outlier: 5.949A  pdb=" N   GLN A  78 " --> pdb=" O   VAL A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 106
      removed outlier: 3.571A  pdb=" N   LEU A 106 " --> pdb=" O   GLU A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 137
    Processing helix  chain 'A' and resid 157 through 171
    Processing helix  chain 'A' and resid 203 through 208
    Processing helix  chain 'A' and resid 249 through 254
    Processing helix  chain 'A' and resid 266 through 278
    Processing helix  chain 'A' and resid 299 through 306
      removed outlier: 3.897A  pdb=" N   LEU A 306 " --> pdb=" O   CYS A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 320
    Processing helix  chain 'A' and resid 326 through 342
    Processing helix  chain 'A' and resid 399 through 403
    Processing helix  chain 'A' and resid 404 through 425
      removed outlier: 3.941A  pdb=" N   GLU A 425 " --> pdb=" O   LYS A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 444
      removed outlier: 4.020A  pdb=" N   VAL A 432 " --> pdb=" O   GLU A 428 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   SER A 444 " --> pdb=" O   TYR A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 465
    Processing helix  chain 'A' and resid 475 through 480
      removed outlier: 3.840A  pdb=" N   ARG A 480 " --> pdb=" O   ASN A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1577 through 1588
    Processing helix  chain 'A' and resid 1607 through 1618
      removed outlier: 3.861A  pdb=" N   CYS A1611 " --> pdb=" O   GLY A1607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1623 through 1629
      removed outlier: 4.035A  pdb=" N   GLN A1628 " --> pdb=" O   SER A1625 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1631 through 1647
    Processing helix  chain 'A' and resid 1654 through 1661
    Processing helix  chain 'A' and resid 1663 through 1678
      removed outlier: 4.261A  pdb=" N   LEU A1667 " --> pdb=" O   ASP A1663 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   PHE A1674 " --> pdb=" O   TYR A1670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2839 through 2841
      No H-bonds generated for 'chain 'A' and resid 2839 through 2841'
    Processing helix  chain 'A' and resid 4116 through 4160
      removed outlier: 3.968A  pdb=" N   ALA A4156 " --> pdb=" O   LYS A4152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4164 through 4209
    Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 177
      removed outlier: 3.511A  pdb=" N   GLU A 114 " --> pdb=" O   HIS A 176 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   VAL A  90 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 126
    Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 185
      removed outlier: 6.093A  pdb=" N   GLN A 197 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   LEU A 184 " --> pdb=" O   ARG A 195 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ARG A 195 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 229 through 232
    Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 287
      removed outlier: 4.044A  pdb=" N   ILE A 238 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ASP A 360 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2843 through 2845
      removed outlier: 3.835A  pdb=" N   LEU A2844 " --> pdb=" O   PHE A2851 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE A2851 " --> pdb=" O   LEU A2844 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    291 hydrogen bonds defined for protein.
    819 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1036
        1.32 -     1.45: 1553
        1.45 -     1.57: 3377
        1.57 -     1.69: 4
        1.69 -     1.81: 36
  Bond restraints: 6006
  Sorted by residual:
  bond pdb=" CA  LYS A 299 "
       pdb=" C   LYS A 299 "
    ideal  model  delta    sigma   weight residual
    1.523  1.463  0.061 1.24e-02 6.50e+03 2.40e+01
  bond pdb=" C2  FAD A4303 "
       pdb=" N3  FAD A4303 "
    ideal  model  delta    sigma   weight residual
    1.399  1.316  0.083 2.00e-02 2.50e+03 1.71e+01
  bond pdb=" O3P FAD A4303 "
       pdb=" P   FAD A4303 "
    ideal  model  delta    sigma   weight residual
    1.660  1.580  0.080 2.00e-02 2.50e+03 1.60e+01
  bond pdb=" O5' FAD A4303 "
       pdb=" P   FAD A4303 "
    ideal  model  delta    sigma   weight residual
    1.637  1.565  0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" C4A FAD A4303 "
       pdb=" C5A FAD A4303 "
    ideal  model  delta    sigma   weight residual
    1.386  1.458 -0.072 2.00e-02 2.50e+03 1.29e+01
  ... (remaining 6001 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.29: 8033
        3.29 -     6.58: 91
        6.58 -     9.88: 19
        9.88 -    13.17: 4
       13.17 -    16.46: 1
  Bond angle restraints: 8148
  Sorted by residual:
  angle pdb=" N   ALA A 298 "
        pdb=" CA  ALA A 298 "
        pdb=" C   ALA A 298 "
      ideal   model   delta    sigma   weight residual
     108.45  118.75  -10.30 1.26e+00 6.30e-01 6.68e+01
  angle pdb=" C   LYS A 300 "
        pdb=" N   GLN A 301 "
        pdb=" CA  GLN A 301 "
      ideal   model   delta    sigma   weight residual
     121.66  109.41   12.25 1.76e+00 3.23e-01 4.84e+01
  angle pdb=" N   LYS A 300 "
        pdb=" CA  LYS A 300 "
        pdb=" C   LYS A 300 "
      ideal   model   delta    sigma   weight residual
     111.33  119.66   -8.33 1.21e+00 6.83e-01 4.74e+01
  angle pdb=" N   PHE A 399 "
        pdb=" CA  PHE A 399 "
        pdb=" C   PHE A 399 "
      ideal   model   delta    sigma   weight residual
     109.76   99.40   10.36 1.59e+00 3.96e-01 4.24e+01
  angle pdb=" CA  PRO A 398 "
        pdb=" N   PRO A 398 "
        pdb=" CD  PRO A 398 "
      ideal   model   delta    sigma   weight residual
     112.00  103.68    8.32 1.40e+00 5.10e-01 3.53e+01
  ... (remaining 8143 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.71: 3433
       28.71 -    57.41: 133
       57.41 -    86.12: 16
       86.12 -   114.83: 3
      114.83 -   143.53: 1
  Dihedral angle restraints: 3586
    sinusoidal: 1466
      harmonic: 2120
  Sorted by residual:
  dihedral pdb=" CA  TYR A2839 "
           pdb=" C   TYR A2839 "
           pdb=" N   VAL A2840 "
           pdb=" CA  VAL A2840 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.07  -28.93     0      5.00e+00 4.00e-02 3.35e+01
  dihedral pdb=" CA  CYS A2881 "
           pdb=" C   CYS A2881 "
           pdb=" N   LEU A2882 "
           pdb=" CA  LEU A2882 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.60  -23.40     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" CA  HIS A2849 "
           pdb=" C   HIS A2849 "
           pdb=" N   PHE A2850 "
           pdb=" CA  PHE A2850 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.20  -22.80     0      5.00e+00 4.00e-02 2.08e+01
  ... (remaining 3583 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 828
       0.093 -    0.187: 60
       0.187 -    0.280: 1
       0.280 -    0.373: 1
       0.373 -    0.467: 2
  Chirality restraints: 892
  Sorted by residual:
  chirality pdb=" CA  LYS A 300 "
            pdb=" N   LYS A 300 "
            pdb=" C   LYS A 300 "
            pdb=" CB  LYS A 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.44e+00
  chirality pdb=" CA  TRP A 400 "
            pdb=" N   TRP A 400 "
            pdb=" C   TRP A 400 "
            pdb=" CB  TRP A 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CA  PHE A 399 "
            pdb=" N   PHE A 399 "
            pdb=" C   PHE A 399 "
            pdb=" CB  PHE A 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.08e+00
  ... (remaining 889 not shown)

  Planarity restraints: 1048
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 466 "    0.066 5.00e-02 4.00e+02   9.93e-02 1.58e+01
        pdb=" N   PRO A 467 "   -0.172 5.00e-02 4.00e+02
        pdb=" CA  PRO A 467 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO A 467 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 447 "    0.062 5.00e-02 4.00e+02   9.33e-02 1.39e+01
        pdb=" N   PRO A 448 "   -0.161 5.00e-02 4.00e+02
        pdb=" CA  PRO A 448 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO A 448 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A2884 "   -0.023 2.00e-02 2.50e+03   2.82e-02 1.19e+01
        pdb=" CG  HIS A2884 "    0.060 2.00e-02 2.50e+03
        pdb=" ND1 HIS A2884 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 HIS A2884 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE1 HIS A2884 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE2 HIS A2884 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1045 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 146
        2.69 -     3.24: 6183
        3.24 -     3.79: 9506
        3.79 -     4.35: 11883
        4.35 -     4.90: 18507
  Nonbonded interactions: 46225
  Sorted by model distance:
  nonbonded pdb=" N   HIS A2852 "
            pdb="ZN    ZN A4301 "
     model   vdw
     2.136 2.310
  nonbonded pdb=" OD1 ASP A1599 "
            pdb=" OG  SER A1602 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OD1 ASP A 415 "
            pdb=" NH1 ARG A 465 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" CD2 HIS A2884 "
            pdb="ZN    ZN A4302 "
     model   vdw
     2.227 1.960
  nonbonded pdb=" O   ILE A1668 "
            pdb=" OG  SER A1672 "
     model   vdw
     2.240 3.040
  ... (remaining 46220 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.570
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.740
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  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:   22.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5935
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      :  0.006   0.136   6006  Z= 0.395
  Angle     :  0.966  16.458   8148  Z= 0.522
  Chirality :  0.054   0.467    892
  Planarity :  0.007   0.099   1048
  Dihedral  : 15.515 143.532   2222
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 21.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  0.33 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.44 (0.31), residues: 733
  helix:  0.08 (0.28), residues: 323
  sheet: -0.22 (0.53), residues: 83
  loop : -0.53 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A1638 
 HIS   0.034   0.002   HIS A2884 
 PHE   0.026   0.002   PHE A 414 
 TYR   0.029   0.002   TYR A2839 
 ARG   0.012   0.001   ARG A1616 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 PHE cc_start: 0.6810 (t80) cc_final: 0.6536 (t80)
REVERT: A   32 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7217 (mt-10)
REVERT: A  153 ASP cc_start: 0.7675 (m-30) cc_final: 0.7356 (m-30)
REVERT: A  284 ILE cc_start: 0.7545 (tp) cc_final: 0.7196 (tp)
REVERT: A  422 ARG cc_start: 0.7102 (tpm170) cc_final: 0.6899 (tpm170)
REVERT: A  449 GLU cc_start: 0.5476 (tp30) cc_final: 0.5252 (tp30)
REVERT: A 1615 TYR cc_start: 0.8017 (t80) cc_final: 0.7519 (t80)
REVERT: A 1644 GLU cc_start: 0.5523 (tp30) cc_final: 0.5115 (tm-30)
REVERT: A 2836 GLU cc_start: 0.7770 (tp30) cc_final: 0.7375 (tp30)
REVERT: A 4152 LYS cc_start: 0.8052 (pptt) cc_final: 0.7744 (pptt)
REVERT: A 4183 ASN cc_start: 0.8124 (m110) cc_final: 0.7832 (m110)
  outliers start: 2
  outliers final: 0
  residues processed: 115
  average time/residue: 0.2408
  time to fit residues: 34.2834
Evaluate side-chains
  106 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0970
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0050
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0470
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 43 optimal weight:    0.0670
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.1828

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A4205 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.188327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.162674 restraints weight = 12024.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.167396 restraints weight = 7924.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.171038 restraints weight = 5626.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.4379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5873
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6006  Z= 0.201
  Angle     :  0.692   8.229   8148  Z= 0.345
  Chirality :  0.044   0.172    892
  Planarity :  0.005   0.064   1048
  Dihedral  :  9.848 146.967    846
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 10.16 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.03 (0.31), residues: 733
  helix:  0.66 (0.29), residues: 330
  sheet: -0.31 (0.50), residues: 90
  loop : -0.46 (0.37), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1638 
 HIS   0.019   0.002   HIS A2884 
 PHE   0.017   0.002   PHE A2851 
 TYR   0.022   0.002   TYR A2839 
 ARG   0.005   0.000   ARG A  80 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 PHE cc_start: 0.6862 (t80) cc_final: 0.6611 (t80)
REVERT: A   28 SER cc_start: 0.7631 (t) cc_final: 0.6928 (t)
REVERT: A   32 GLU cc_start: 0.7744 (mt-10) cc_final: 0.6977 (mt-10)
REVERT: A  153 ASP cc_start: 0.7700 (m-30) cc_final: 0.7438 (m-30)
REVERT: A  322 SER cc_start: 0.8464 (p) cc_final: 0.8195 (t)
REVERT: A  375 SER cc_start: 0.7523 (p) cc_final: 0.7091 (p)
REVERT: A  422 ARG cc_start: 0.7251 (tpm170) cc_final: 0.6959 (tpm170)
REVERT: A 1615 TYR cc_start: 0.8088 (t80) cc_final: 0.7564 (t80)
REVERT: A 1616 ARG cc_start: 0.8159 (ttt-90) cc_final: 0.7740 (ttt-90)
REVERT: A 2836 GLU cc_start: 0.7609 (tp30) cc_final: 0.7234 (tp30)
REVERT: A 4152 LYS cc_start: 0.8016 (pptt) cc_final: 0.7616 (pptt)
REVERT: A 4183 ASN cc_start: 0.8116 (m110) cc_final: 0.7869 (m110)
  outliers start: 8
  outliers final: 5
  residues processed: 108
  average time/residue: 0.2202
  time to fit residues: 30.2302
Evaluate side-chains
  106 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue 1585 CYS
Chi-restraints excluded: chain A residue 2840 VAL
Chi-restraints excluded: chain A residue 4202 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 18 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 43 optimal weight:    0.1980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 HIS
** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1673 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 = 0.4569 r_free = 0.4569 target = 0.187037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.160908 restraints weight = 11756.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.165682 restraints weight = 7605.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.169258 restraints weight = 5380.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.4351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5910
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6006  Z= 0.190
  Angle     :  0.627   8.881   8148  Z= 0.309
  Chirality :  0.042   0.168    892
  Planarity :  0.005   0.058   1048
  Dihedral  :  9.642 149.620    846
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 13.11 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.16 (0.31), residues: 733
  helix:  0.78 (0.29), residues: 330
  sheet: -0.27 (0.51), residues: 91
  loop : -0.39 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1638 
 HIS   0.010   0.001   HIS A2884 
 PHE   0.010   0.001   PHE A 399 
 TYR   0.017   0.002   TYR A2839 
 ARG   0.004   0.000   ARG A2843 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.3561 (mm-30)
REVERT: A   17 PHE cc_start: 0.6939 (t80) cc_final: 0.6653 (t80)
REVERT: A   28 SER cc_start: 0.7626 (t) cc_final: 0.6948 (t)
REVERT: A   32 GLU cc_start: 0.7738 (mt-10) cc_final: 0.6950 (mt-10)
REVERT: A   49 HIS cc_start: 0.7765 (m90) cc_final: 0.7429 (m90)
REVERT: A  153 ASP cc_start: 0.7723 (m-30) cc_final: 0.7472 (m-30)
REVERT: A  164 LEU cc_start: 0.7447 (mt) cc_final: 0.6993 (tt)
REVERT: A  170 LEU cc_start: 0.7450 (tp) cc_final: 0.7176 (tt)
REVERT: A  422 ARG cc_start: 0.7389 (tpm170) cc_final: 0.7006 (tpm170)
REVERT: A 1615 TYR cc_start: 0.8172 (t80) cc_final: 0.7656 (t80)
REVERT: A 1644 GLU cc_start: 0.5396 (tp30) cc_final: 0.5056 (tm-30)
REVERT: A 2849 HIS cc_start: 0.7995 (t70) cc_final: 0.7516 (t70)
REVERT: A 4152 LYS cc_start: 0.8042 (pptt) cc_final: 0.7645 (pptt)
REVERT: A 4174 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6560 (pt0)
REVERT: A 4176 LEU cc_start: 0.5437 (OUTLIER) cc_final: 0.4726 (mt)
REVERT: A 4203 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8136 (mm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 122
  average time/residue: 0.1919
  time to fit residues: 30.3461
Evaluate side-chains
  120 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue 1585 CYS
Chi-restraints excluded: chain A residue 1589 THR
Chi-restraints excluded: chain A residue 2837 HIS
Chi-restraints excluded: chain A residue 2840 VAL
Chi-restraints excluded: chain A residue 4174 GLN
Chi-restraints excluded: chain A residue 4176 LEU
Chi-restraints excluded: chain A residue 4202 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1586 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.186523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.160621 restraints weight = 11983.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.165340 restraints weight = 7820.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.168771 restraints weight = 5547.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.4342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5933
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6006  Z= 0.200
  Angle     :  0.632   9.589   8148  Z= 0.310
  Chirality :  0.042   0.212    892
  Planarity :  0.005   0.052   1048
  Dihedral  :  9.573 151.781    846
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.05 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.23 (0.31), residues: 733
  helix:  0.87 (0.29), residues: 331
  sheet: -0.22 (0.51), residues: 89
  loop : -0.41 (0.37), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1638 
 HIS   0.006   0.001   HIS A2884 
 PHE   0.011   0.001   PHE A 399 
 TYR   0.014   0.002   TYR A 286 
 ARG   0.005   0.000   ARG A2843 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.3464 (mm-30)
REVERT: A   17 PHE cc_start: 0.6875 (t80) cc_final: 0.6579 (t80)
REVERT: A   28 SER cc_start: 0.7626 (t) cc_final: 0.6924 (t)
REVERT: A   32 GLU cc_start: 0.7728 (mt-10) cc_final: 0.6928 (mt-10)
REVERT: A   49 HIS cc_start: 0.7865 (m90) cc_final: 0.7576 (m90)
REVERT: A   97 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5246 (mp)
REVERT: A  153 ASP cc_start: 0.7733 (m-30) cc_final: 0.7486 (m-30)
REVERT: A  164 LEU cc_start: 0.7508 (mt) cc_final: 0.7104 (tt)
REVERT: A  170 LEU cc_start: 0.7455 (tp) cc_final: 0.7147 (tt)
REVERT: A  422 ARG cc_start: 0.7344 (tpm170) cc_final: 0.6928 (tpm170)
REVERT: A  423 TRP cc_start: 0.6467 (t60) cc_final: 0.6026 (t60)
REVERT: A  449 GLU cc_start: 0.5690 (tp30) cc_final: 0.5418 (tp30)
REVERT: A  458 TYR cc_start: 0.7105 (m-10) cc_final: 0.6869 (m-80)
REVERT: A 1615 TYR cc_start: 0.8081 (t80) cc_final: 0.7559 (t80)
REVERT: A 1616 ARG cc_start: 0.7909 (ttt-90) cc_final: 0.7405 (ttt-90)
REVERT: A 2836 GLU cc_start: 0.7382 (tp30) cc_final: 0.7118 (tp30)
REVERT: A 4152 LYS cc_start: 0.8053 (pptt) cc_final: 0.7621 (pptt)
REVERT: A 4176 LEU cc_start: 0.5443 (OUTLIER) cc_final: 0.4732 (mt)
REVERT: A 4183 ASN cc_start: 0.8353 (m-40) cc_final: 0.8140 (m110)
  outliers start: 17
  outliers final: 10
  residues processed: 117
  average time/residue: 0.1980
  time to fit residues: 29.8501
Evaluate side-chains
  120 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue 1585 CYS
Chi-restraints excluded: chain A residue 2837 HIS
Chi-restraints excluded: chain A residue 4176 LEU
Chi-restraints excluded: chain A residue 4202 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    0.4980
   chunk 39 optimal weight:    0.4980
   chunk 4 optimal weight:    0.3980
   chunk 3 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0980
   chunk 23 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  73 GLN
** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4174 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.188444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.162083 restraints weight = 11768.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.166844 restraints weight = 7751.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.170316 restraints weight = 5532.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.4362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5890
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6006  Z= 0.163
  Angle     :  0.606  10.635   8148  Z= 0.294
  Chirality :  0.042   0.224    892
  Planarity :  0.005   0.048   1048
  Dihedral  :  9.508 151.439    846
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 16.89 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.34 (0.31), residues: 733
  helix:  1.06 (0.29), residues: 330
  sheet: -0.33 (0.51), residues: 91
  loop : -0.40 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A1638 
 HIS   0.007   0.001   HIS A2884 
 PHE   0.009   0.001   PHE A 399 
 TYR   0.012   0.002   TYR A2839 
 ARG   0.004   0.000   ARG A2843 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.3202 (mm-30)
REVERT: A   28 SER cc_start: 0.7660 (t) cc_final: 0.6991 (t)
REVERT: A   32 GLU cc_start: 0.7690 (mt-10) cc_final: 0.6912 (mt-10)
REVERT: A   40 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7494 (tm-30)
REVERT: A   49 HIS cc_start: 0.7839 (m90) cc_final: 0.7498 (m90)
REVERT: A   97 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5171 (mp)
REVERT: A  153 ASP cc_start: 0.7705 (m-30) cc_final: 0.7479 (m-30)
REVERT: A  164 LEU cc_start: 0.7494 (mt) cc_final: 0.7052 (tt)
REVERT: A  400 TRP cc_start: 0.7035 (m-10) cc_final: 0.6630 (m-10)
REVERT: A  422 ARG cc_start: 0.7324 (tpm170) cc_final: 0.6939 (tpm170)
REVERT: A  423 TRP cc_start: 0.6395 (t60) cc_final: 0.6009 (t60)
REVERT: A  458 TYR cc_start: 0.6960 (m-10) cc_final: 0.6221 (m-80)
REVERT: A 1615 TYR cc_start: 0.8084 (t80) cc_final: 0.7551 (t80)
REVERT: A 1616 ARG cc_start: 0.7851 (ttt-90) cc_final: 0.7382 (ttt-90)
REVERT: A 1671 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6293 (mp)
REVERT: A 4152 LYS cc_start: 0.8051 (pptt) cc_final: 0.7690 (pptt)
REVERT: A 4176 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.4643 (mt)
REVERT: A 4183 ASN cc_start: 0.8379 (m-40) cc_final: 0.8144 (m110)
REVERT: A 4189 GLU cc_start: 0.8008 (pt0) cc_final: 0.7648 (pt0)
REVERT: A 4191 GLU cc_start: 0.8643 (pp20) cc_final: 0.8189 (pp20)
  outliers start: 22
  outliers final: 12
  residues processed: 123
  average time/residue: 0.2338
  time to fit residues: 37.0569
Evaluate side-chains
  127 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue 1585 CYS
Chi-restraints excluded: chain A residue 1589 THR
Chi-restraints excluded: chain A residue 1671 LEU
Chi-restraints excluded: chain A residue 2837 HIS
Chi-restraints excluded: chain A residue 4176 LEU
Chi-restraints excluded: chain A residue 4202 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0070
   chunk 14 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.7600

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1586 GLN
A2859 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.187334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.160506 restraints weight = 11833.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.165192 restraints weight = 7832.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.168666 restraints weight = 5627.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.4337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5925
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6006  Z= 0.193
  Angle     :  0.630  10.909   8148  Z= 0.304
  Chirality :  0.042   0.226    892
  Planarity :  0.004   0.047   1048
  Dihedral  :  9.454 152.818    846
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 17.21 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.37 (0.31), residues: 733
  helix:  1.05 (0.28), residues: 330
  sheet: -0.12 (0.52), residues: 87
  loop : -0.42 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A1638 
 HIS   0.006   0.001   HIS A2884 
 PHE   0.011   0.001   PHE A 399 
 TYR   0.018   0.002   TYR A2839 
 ARG   0.005   0.000   ARG A 465 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.3078 (mm-30)
REVERT: A   28 SER cc_start: 0.7629 (t) cc_final: 0.6988 (t)
REVERT: A   32 GLU cc_start: 0.7705 (mt-10) cc_final: 0.6966 (mt-10)
REVERT: A   40 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7450 (tm-30)
REVERT: A   49 HIS cc_start: 0.7895 (m90) cc_final: 0.7596 (m90)
REVERT: A   97 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5178 (mp)
REVERT: A  153 ASP cc_start: 0.7663 (m-30) cc_final: 0.7420 (m-30)
REVERT: A  164 LEU cc_start: 0.7495 (mt) cc_final: 0.7104 (tt)
REVERT: A  400 TRP cc_start: 0.7181 (m-10) cc_final: 0.6806 (m-10)
REVERT: A  422 ARG cc_start: 0.7291 (tpm170) cc_final: 0.6915 (tpm170)
REVERT: A  423 TRP cc_start: 0.6489 (t60) cc_final: 0.6090 (t60)
REVERT: A  433 LEU cc_start: 0.5955 (mp) cc_final: 0.5263 (mt)
REVERT: A  465 ARG cc_start: 0.5939 (ptp-170) cc_final: 0.5564 (ptp-170)
REVERT: A 1615 TYR cc_start: 0.8073 (t80) cc_final: 0.7549 (t80)
REVERT: A 1616 ARG cc_start: 0.7821 (ttt-90) cc_final: 0.7325 (ttt-90)
REVERT: A 1671 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6380 (mp)
REVERT: A 4152 LYS cc_start: 0.8095 (pptt) cc_final: 0.7698 (pptt)
REVERT: A 4183 ASN cc_start: 0.8388 (m-40) cc_final: 0.8172 (m-40)
REVERT: A 4189 GLU cc_start: 0.8025 (pt0) cc_final: 0.7615 (pt0)
REVERT: A 4191 GLU cc_start: 0.8626 (pp20) cc_final: 0.8152 (pp20)
  outliers start: 22
  outliers final: 15
  residues processed: 124
  average time/residue: 0.2049
  time to fit residues: 32.8859
Evaluate side-chains
  124 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  483 TYR
Chi-restraints excluded: chain A residue 1589 THR
Chi-restraints excluded: chain A residue 1658 VAL
Chi-restraints excluded: chain A residue 1671 LEU
Chi-restraints excluded: chain A residue 2837 HIS
Chi-restraints excluded: chain A residue 2846 VAL
Chi-restraints excluded: chain A residue 4202 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 379 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 = 0.4543 r_free = 0.4543 target = 0.184757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.158239 restraints weight = 11940.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.162978 restraints weight = 7902.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.166478 restraints weight = 5660.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5974
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6006  Z= 0.238
  Angle     :  0.668  11.542   8148  Z= 0.325
  Chirality :  0.043   0.233    892
  Planarity :  0.005   0.058   1048
  Dihedral  :  9.514 154.493    846
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.87 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.33 (0.31), residues: 733
  helix:  1.05 (0.29), residues: 331
  sheet: -0.20 (0.52), residues: 87
  loop : -0.47 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A1638 
 HIS   0.005   0.001   HIS A 343 
 PHE   0.012   0.001   PHE A 399 
 TYR   0.016   0.002   TYR A 286 
 ARG   0.005   0.000   ARG A 472 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.3083 (mm-30)
REVERT: A   28 SER cc_start: 0.7649 (t) cc_final: 0.7033 (t)
REVERT: A   32 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7011 (mt-10)
REVERT: A   40 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7460 (tm-30)
REVERT: A   49 HIS cc_start: 0.7843 (m90) cc_final: 0.7541 (m90)
REVERT: A  153 ASP cc_start: 0.7697 (m-30) cc_final: 0.7422 (m-30)
REVERT: A  400 TRP cc_start: 0.7311 (m-10) cc_final: 0.6921 (m-10)
REVERT: A  422 ARG cc_start: 0.7308 (tpm170) cc_final: 0.6888 (tpm170)
REVERT: A  433 LEU cc_start: 0.6028 (mp) cc_final: 0.5515 (mt)
REVERT: A  449 GLU cc_start: 0.5848 (tp30) cc_final: 0.5579 (tp30)
REVERT: A  458 TYR cc_start: 0.6551 (m-80) cc_final: 0.6312 (m-80)
REVERT: A  465 ARG cc_start: 0.6071 (ptp-170) cc_final: 0.5811 (ptp-170)
REVERT: A 1615 TYR cc_start: 0.8123 (t80) cc_final: 0.7611 (t80)
REVERT: A 1616 ARG cc_start: 0.7660 (ttt-90) cc_final: 0.7173 (ttt-90)
REVERT: A 1644 GLU cc_start: 0.5414 (tp30) cc_final: 0.5110 (tm-30)
REVERT: A 1671 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6492 (mp)
REVERT: A 4152 LYS cc_start: 0.8161 (pptt) cc_final: 0.7776 (pptt)
REVERT: A 4176 LEU cc_start: 0.5490 (OUTLIER) cc_final: 0.4778 (mt)
REVERT: A 4189 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7609 (pt0)
REVERT: A 4191 GLU cc_start: 0.8612 (pp20) cc_final: 0.8118 (pp20)
  outliers start: 21
  outliers final: 15
  residues processed: 119
  average time/residue: 0.2263
  time to fit residues: 33.9288
Evaluate side-chains
  127 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  483 TYR
Chi-restraints excluded: chain A residue 1589 THR
Chi-restraints excluded: chain A residue 1658 VAL
Chi-restraints excluded: chain A residue 1659 VAL
Chi-restraints excluded: chain A residue 1671 LEU
Chi-restraints excluded: chain A residue 2837 HIS
Chi-restraints excluded: chain A residue 2839 TYR
Chi-restraints excluded: chain A residue 2846 VAL
Chi-restraints excluded: chain A residue 4176 LEU
Chi-restraints excluded: chain A residue 4189 GLU
Chi-restraints excluded: chain A residue 4202 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 35 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0980
   chunk 38 optimal weight:    0.7980
   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  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 379 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 = 0.4559 r_free = 0.4559 target = 0.186120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.159457 restraints weight = 11841.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.164073 restraints weight = 7850.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.167638 restraints weight = 5673.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5940
moved from start:          0.2661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6006  Z= 0.197
  Angle     :  0.657  11.754   8148  Z= 0.317
  Chirality :  0.042   0.211    892
  Planarity :  0.005   0.060   1048
  Dihedral  :  9.467 152.818    846
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 18.52 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.31), residues: 733
  helix:  1.11 (0.29), residues: 332
  sheet:  0.04 (0.53), residues: 85
  loop : -0.49 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A1638 
 HIS   0.003   0.001   HIS A2884 
 PHE   0.010   0.001   PHE A 399 
 TYR   0.013   0.002   TYR A 286 
 ARG   0.004   0.000   ARG A 472 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.3132 (mm-30)
REVERT: A   28 SER cc_start: 0.7568 (t) cc_final: 0.6906 (t)
REVERT: A   32 GLU cc_start: 0.7627 (mt-10) cc_final: 0.6896 (mt-10)
REVERT: A   40 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7422 (tm-30)
REVERT: A   49 HIS cc_start: 0.7816 (m90) cc_final: 0.7512 (m90)
REVERT: A  153 ASP cc_start: 0.7674 (m-30) cc_final: 0.7424 (m-30)
REVERT: A  349 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5735 (mp)
REVERT: A  400 TRP cc_start: 0.7365 (m-10) cc_final: 0.7005 (m-10)
REVERT: A  422 ARG cc_start: 0.7285 (tpm170) cc_final: 0.6883 (tpm170)
REVERT: A  433 LEU cc_start: 0.5881 (mp) cc_final: 0.5167 (mt)
REVERT: A  458 TYR cc_start: 0.6579 (m-80) cc_final: 0.6376 (m-80)
REVERT: A  465 ARG cc_start: 0.5880 (ptp-170) cc_final: 0.5482 (ptp-170)
REVERT: A 1615 TYR cc_start: 0.8103 (t80) cc_final: 0.7562 (t80)
REVERT: A 1616 ARG cc_start: 0.7749 (ttt-90) cc_final: 0.7221 (ttt-90)
REVERT: A 1671 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6406 (mp)
REVERT: A 4152 LYS cc_start: 0.8135 (pptt) cc_final: 0.7777 (pptt)
REVERT: A 4176 LEU cc_start: 0.5446 (OUTLIER) cc_final: 0.4732 (mt)
REVERT: A 4189 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7561 (pt0)
REVERT: A 4191 GLU cc_start: 0.8648 (pp20) cc_final: 0.8119 (pp20)
  outliers start: 23
  outliers final: 15
  residues processed: 120
  average time/residue: 0.1934
  time to fit residues: 29.9609
Evaluate side-chains
  128 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  483 TYR
Chi-restraints excluded: chain A residue 1589 THR
Chi-restraints excluded: chain A residue 1658 VAL
Chi-restraints excluded: chain A residue 1659 VAL
Chi-restraints excluded: chain A residue 1671 LEU
Chi-restraints excluded: chain A residue 2837 HIS
Chi-restraints excluded: chain A residue 2839 TYR
Chi-restraints excluded: chain A residue 4176 LEU
Chi-restraints excluded: chain A residue 4189 GLU
Chi-restraints excluded: chain A residue 4202 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 17 optimal weight:    0.1980
   chunk 45 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1578 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 = 0.4539 r_free = 0.4539 target = 0.184479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.157564 restraints weight = 11997.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.162148 restraints weight = 7992.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.165736 restraints weight = 5792.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.4305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5991
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6006  Z= 0.240
  Angle     :  0.702  11.778   8148  Z= 0.340
  Chirality :  0.043   0.243    892
  Planarity :  0.005   0.060   1048
  Dihedral  :  9.516 156.370    846
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.34 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.39 (0.31), residues: 733
  helix:  1.07 (0.29), residues: 332
  sheet:  0.07 (0.53), residues: 85
  loop : -0.48 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A1638 
 HIS   0.005   0.001   HIS A 343 
 PHE   0.012   0.001   PHE A1674 
 TYR   0.016   0.002   TYR A 286 
 ARG   0.006   0.000   ARG A 472 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.3148 (mm-30)
REVERT: A   28 SER cc_start: 0.7649 (t) cc_final: 0.7002 (t)
REVERT: A   32 GLU cc_start: 0.7675 (mt-10) cc_final: 0.6934 (mt-10)
REVERT: A   40 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7425 (tm-30)
REVERT: A  153 ASP cc_start: 0.7695 (m-30) cc_final: 0.7404 (m-30)
REVERT: A  400 TRP cc_start: 0.7541 (m-10) cc_final: 0.7174 (m-10)
REVERT: A  422 ARG cc_start: 0.7291 (tpm170) cc_final: 0.6838 (tpm170)
REVERT: A  433 LEU cc_start: 0.5892 (mp) cc_final: 0.5177 (mt)
REVERT: A  449 GLU cc_start: 0.5860 (tp30) cc_final: 0.5552 (tp30)
REVERT: A 1615 TYR cc_start: 0.8153 (t80) cc_final: 0.7506 (t80)
REVERT: A 1644 GLU cc_start: 0.5586 (tp30) cc_final: 0.5256 (tm-30)
REVERT: A 1671 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6454 (mp)
REVERT: A 4152 LYS cc_start: 0.8175 (pptt) cc_final: 0.7972 (pptt)
REVERT: A 4189 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7515 (pt0)
REVERT: A 4191 GLU cc_start: 0.8657 (pp20) cc_final: 0.8146 (pp20)
  outliers start: 20
  outliers final: 15
  residues processed: 114
  average time/residue: 0.2021
  time to fit residues: 29.5149
Evaluate side-chains
  122 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  483 TYR
Chi-restraints excluded: chain A residue 1585 CYS
Chi-restraints excluded: chain A residue 1589 THR
Chi-restraints excluded: chain A residue 1658 VAL
Chi-restraints excluded: chain A residue 1671 LEU
Chi-restraints excluded: chain A residue 2837 HIS
Chi-restraints excluded: chain A residue 2839 TYR
Chi-restraints excluded: chain A residue 2846 VAL
Chi-restraints excluded: chain A residue 4189 GLU
Chi-restraints excluded: chain A residue 4202 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 35 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 57 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 GLN
** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.186470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.159666 restraints weight = 12100.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.164409 restraints weight = 8016.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.167981 restraints weight = 5783.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.4337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5930
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6006  Z= 0.188
  Angle     :  0.684  12.135   8148  Z= 0.327
  Chirality :  0.043   0.248    892
  Planarity :  0.005   0.062   1048
  Dihedral  :  9.483 156.931    846
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 20.00 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.37 (0.32), residues: 733
  helix:  1.05 (0.29), residues: 338
  sheet:  0.06 (0.53), residues: 86
  loop : -0.53 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A1638 
 HIS   0.003   0.001   HIS A 452 
 PHE   0.013   0.001   PHE A1674 
 TYR   0.012   0.002   TYR A 265 
 ARG   0.005   0.000   ARG A 465 

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

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

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1466 Ramachandran restraints generated.
    733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.2971 (mm-30)
REVERT: A   28 SER cc_start: 0.7666 (t) cc_final: 0.6982 (t)
REVERT: A   32 GLU cc_start: 0.7690 (mt-10) cc_final: 0.6936 (mt-10)
REVERT: A   40 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7397 (tm-30)
REVERT: A  153 ASP cc_start: 0.7646 (m-30) cc_final: 0.7409 (m-30)
REVERT: A  164 LEU cc_start: 0.7686 (mt) cc_final: 0.7137 (tt)
REVERT: A  301 GLN cc_start: 0.5810 (OUTLIER) cc_final: 0.5357 (pp30)
REVERT: A  400 TRP cc_start: 0.7532 (m-10) cc_final: 0.7142 (m-10)
REVERT: A  422 ARG cc_start: 0.7256 (tpm170) cc_final: 0.6884 (tpm170)
REVERT: A  433 LEU cc_start: 0.5728 (mp) cc_final: 0.5019 (mt)
REVERT: A  449 GLU cc_start: 0.5759 (tp30) cc_final: 0.5461 (tp30)
REVERT: A 1615 TYR cc_start: 0.8085 (t80) cc_final: 0.7513 (t80)
REVERT: A 1616 ARG cc_start: 0.7653 (ttt-90) cc_final: 0.7077 (ttt-90)
REVERT: A 1644 GLU cc_start: 0.5418 (tp30) cc_final: 0.5084 (tm-30)
REVERT: A 1671 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6586 (mp)
REVERT: A 4189 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7501 (pt0)
REVERT: A 4191 GLU cc_start: 0.8639 (pp20) cc_final: 0.8119 (pp20)
  outliers start: 18
  outliers final: 13
  residues processed: 120
  average time/residue: 0.2159
  time to fit residues: 33.7640
Evaluate side-chains
  126 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  130 PHE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  483 TYR
Chi-restraints excluded: chain A residue 1589 THR
Chi-restraints excluded: chain A residue 1659 VAL
Chi-restraints excluded: chain A residue 1671 LEU
Chi-restraints excluded: chain A residue 2837 HIS
Chi-restraints excluded: chain A residue 2839 TYR
Chi-restraints excluded: chain A residue 2846 VAL
Chi-restraints excluded: chain A residue 4189 GLU
Chi-restraints excluded: chain A residue 4202 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
** A 379 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 = 0.4536 r_free = 0.4536 target = 0.184728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.158315 restraints weight = 12116.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.163072 restraints weight = 8063.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.166666 restraints weight = 5811.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5952
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6006  Z= 0.211
  Angle     :  0.699  12.575   8148  Z= 0.337
  Chirality :  0.044   0.248    892
  Planarity :  0.005   0.064   1048
  Dihedral  :  9.492 157.845    846
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.33 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.42 (0.32), residues: 733
  helix:  1.05 (0.29), residues: 338
  sheet:  0.18 (0.53), residues: 85
  loop : -0.48 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A1638 
 HIS   0.005   0.001   HIS A 343 
 PHE   0.019   0.001   PHE A1674 
 TYR   0.018   0.002   TYR A2839 
 ARG   0.005   0.000   ARG A 472 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2050.18 seconds
wall clock time: 37 minutes 55.50 seconds (2275.50 seconds total)