Starting phenix.real_space_refine
on Fri Oct 10 13:18:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y6k_38989/10_2025/8y6k_38989_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y6k_38989/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y6k_38989/10_2025/8y6k_38989_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y6k_38989/10_2025/8y6k_38989_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y6k_38989/10_2025/8y6k_38989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y6k_38989/10_2025/8y6k_38989.map"
  }
  resolution = 3.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.60, per 1000 atoms: 0.27
  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: 0.38
  Conformation dependent library (CDL) restraints added in 317.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  
  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: 0.13
  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: 0.89

  Time building geometry restraints manager: 0.54 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:             0.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.560
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.240
-------------------------------------------------------------------------------
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   0.198   6012  Z= 0.296
  Angle     :  0.976  16.458   8151  Z= 0.523
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.012   0.001   ARG A1616 
 TYR   0.029   0.002   TYR A2839 
 PHE   0.026   0.002   PHE A 414 
 TRP   0.011   0.002   TRP A1638 
 HIS   0.034   0.002   HIS A2884 

Details of bonding type rmsd
  covalent geometry    : bond        0.00579 ( 6006)
  covalent geometry    : angle       0.96584 ( 8148)
  hydrogen bonds       : bond        0.13315 (  291)
  hydrogen bonds       : angle       6.50204 (  819)
  metal coordination   : bond        0.08217 (    6)
  metal coordination   : angle       7.43048 (    3)

*********************** 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  : 0.130 
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: 0.7745 (pptt)
REVERT: A 4183 ASN cc_start: 0.8124 (m110) cc_final: 0.7834 (m110)
  outliers start: 2
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1000
  time to fit residues: 14.4549
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  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.0060
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6196

-------------------------------------------------------------------------------
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 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 = 0.4557 r_free = 0.4557 target = 0.186905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.161285 restraints weight = 11826.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.166003 restraints weight = 7696.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.169465 restraints weight = 5455.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.172134 restraints weight = 4078.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.174064 restraints weight = 3165.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.4399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5855
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.100   6012  Z= 0.147
  Angle     :  0.713   8.259   8151  Z= 0.352
  Chirality :  0.044   0.169    892
  Planarity :  0.005   0.066   1048
  Dihedral  :  9.927 150.177    846
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 15.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 10.00 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.31), residues: 733
  helix:  0.63 (0.29), residues: 330
  sheet: -0.25 (0.50), residues: 88
  loop : -0.50 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  80 
 TYR   0.024   0.002   TYR A2839 
 PHE   0.017   0.002   PHE A2851 
 TRP   0.021   0.001   TRP A1638 
 HIS   0.019   0.001   HIS A2884 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6006)
  covalent geometry    : angle       0.70508 ( 8148)
  hydrogen bonds       : bond        0.04858 (  291)
  hydrogen bonds       : angle       5.50070 (  819)
  metal coordination   : bond        0.04103 (    6)
  metal coordination   : angle       5.60076 (    3)

*********************** 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
  116 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 PHE cc_start: 0.6776 (t80) cc_final: 0.6508 (t80)
REVERT: A   28 SER cc_start: 0.7639 (t) cc_final: 0.6884 (t)
REVERT: A   32 GLU cc_start: 0.7735 (mt-10) cc_final: 0.6980 (mt-10)
REVERT: A  153 ASP cc_start: 0.7775 (m-30) cc_final: 0.7499 (m-30)
REVERT: A  422 ARG cc_start: 0.7278 (tpm170) cc_final: 0.6947 (tpm170)
REVERT: A 1615 TYR cc_start: 0.8093 (t80) cc_final: 0.7563 (t80)
REVERT: A 1616 ARG cc_start: 0.8176 (ttt-90) cc_final: 0.7754 (ttt-90)
REVERT: A 1644 GLU cc_start: 0.5465 (tp30) cc_final: 0.5114 (tm-30)
REVERT: A 2836 GLU cc_start: 0.7599 (tp30) cc_final: 0.7283 (tp30)
REVERT: A 4152 LYS cc_start: 0.8038 (pptt) cc_final: 0.7628 (pptt)
REVERT: A 4183 ASN cc_start: 0.8112 (m110) cc_final: 0.7852 (m110)
  outliers start: 8
  outliers final: 6
  residues processed: 109
  average time/residue: 0.0917
  time to fit residues: 12.7616
Evaluate side-chains
  109 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue 1585 CYS
Chi-restraints excluded: chain A residue 2837 HIS
Chi-restraints excluded: chain A residue 4189 GLU
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 17 optimal weight:    0.8980
   chunk 64 optimal weight:   20.0000
   chunk 14 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0010
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.7390

-------------------------------------------------------------------------------
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 ** 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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.185503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.159838 restraints weight = 12030.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.164537 restraints weight = 7876.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.168023 restraints weight = 5592.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.170526 restraints weight = 4204.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.172506 restraints weight = 3295.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.4394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5867
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6012  Z= 0.138
  Angle     :  0.648   8.806   8151  Z= 0.316
  Chirality :  0.042   0.192    892
  Planarity :  0.005   0.057   1048
  Dihedral  :  9.733 156.855    846
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 13.44 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.31), residues: 733
  helix:  0.71 (0.28), residues: 331
  sheet: -0.23 (0.51), residues: 89
  loop : -0.48 (0.37), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A2843 
 TYR   0.017   0.002   TYR A2839 
 PHE   0.011   0.001   PHE A 399 
 TRP   0.021   0.001   TRP A1638 
 HIS   0.010   0.001   HIS A2884 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6006)
  covalent geometry    : angle       0.64166 ( 8148)
  hydrogen bonds       : bond        0.04249 (  291)
  hydrogen bonds       : angle       5.28882 (  819)
  metal coordination   : bond        0.02674 (    6)
  metal coordination   : angle       4.72294 (    3)

*********************** 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
  129 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.3474 (mm-30)
REVERT: A   17 PHE cc_start: 0.6697 (t80) cc_final: 0.6446 (t80)
REVERT: A   28 SER cc_start: 0.7633 (t) cc_final: 0.6863 (t)
REVERT: A   32 GLU cc_start: 0.7694 (mt-10) cc_final: 0.6899 (mt-10)
REVERT: A   49 HIS cc_start: 0.7813 (m90) cc_final: 0.7520 (m90)
REVERT: A  153 ASP cc_start: 0.7759 (m-30) cc_final: 0.7502 (m-30)
REVERT: A  164 LEU cc_start: 0.7422 (mt) cc_final: 0.7008 (tt)
REVERT: A  422 ARG cc_start: 0.7380 (tpm170) cc_final: 0.6986 (tpm170)
REVERT: A 1582 LEU cc_start: 0.7426 (tt) cc_final: 0.7177 (pp)
REVERT: A 1615 TYR cc_start: 0.8110 (t80) cc_final: 0.7568 (t80)
REVERT: A 1616 ARG cc_start: 0.7948 (ttt-90) cc_final: 0.7473 (ttt-90)
REVERT: A 2836 GLU cc_start: 0.7565 (tp30) cc_final: 0.7250 (tp30)
REVERT: A 2849 HIS cc_start: 0.7976 (t70) cc_final: 0.7522 (t70)
REVERT: A 4152 LYS cc_start: 0.8040 (pptt) cc_final: 0.7633 (pptt)
REVERT: A 4174 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6553 (pt0)
REVERT: A 4176 LEU cc_start: 0.5448 (OUTLIER) cc_final: 0.4305 (mt)
REVERT: A 4183 ASN cc_start: 0.8139 (m110) cc_final: 0.7893 (m110)
  outliers start: 17
  outliers final: 11
  residues processed: 117
  average time/residue: 0.0906
  time to fit residues: 13.6050
Evaluate side-chains
  124 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
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  284 ILE
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 4189 GLU
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 38 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0980
   chunk 18 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0670
   chunk 28 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.4554 r_free = 0.4554 target = 0.186176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.160668 restraints weight = 12039.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.165416 restraints weight = 7842.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.168864 restraints weight = 5536.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.171402 restraints weight = 4133.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.173180 restraints weight = 3231.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.4397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5852
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6012  Z= 0.125
  Angle     :  0.627   9.733   8151  Z= 0.306
  Chirality :  0.042   0.217    892
  Planarity :  0.005   0.053   1048
  Dihedral  :  9.599 154.558    846
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 15.41 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.31), residues: 733
  helix:  0.81 (0.29), residues: 331
  sheet: -0.20 (0.51), residues: 89
  loop : -0.48 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2843 
 TYR   0.013   0.002   TYR A 286 
 PHE   0.009   0.001   PHE A 399 
 TRP   0.022   0.001   TRP A1638 
 HIS   0.005   0.001   HIS A2884 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6006)
  covalent geometry    : angle       0.62180 ( 8148)
  hydrogen bonds       : bond        0.04007 (  291)
  hydrogen bonds       : angle       5.10739 (  819)
  metal coordination   : bond        0.02130 (    6)
  metal coordination   : angle       4.12943 (    3)

*********************** 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
  132 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.3401 (mm-30)
REVERT: A   17 PHE cc_start: 0.6745 (t80) cc_final: 0.6454 (t80)
REVERT: A   28 SER cc_start: 0.7638 (t) cc_final: 0.6873 (t)
REVERT: A   32 GLU cc_start: 0.7683 (mt-10) cc_final: 0.6882 (mt-10)
REVERT: A   49 HIS cc_start: 0.7939 (m90) cc_final: 0.7644 (m90)
REVERT: A   97 LEU cc_start: 0.6006 (OUTLIER) cc_final: 0.5193 (mp)
REVERT: A  153 ASP cc_start: 0.7713 (m-30) cc_final: 0.7482 (m-30)
REVERT: A  164 LEU cc_start: 0.7458 (mt) cc_final: 0.7059 (tt)
REVERT: A  422 ARG cc_start: 0.7307 (tpm170) cc_final: 0.6939 (tpm170)
REVERT: A  423 TRP cc_start: 0.6497 (t60) cc_final: 0.6071 (t60)
REVERT: A  449 GLU cc_start: 0.5622 (tp30) cc_final: 0.5353 (tp30)
REVERT: A  458 TYR cc_start: 0.7080 (m-80) cc_final: 0.6847 (m-80)
REVERT: A 1582 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7090 (pp)
REVERT: A 1615 TYR cc_start: 0.8068 (t80) cc_final: 0.7542 (t80)
REVERT: A 2836 GLU cc_start: 0.7505 (tp30) cc_final: 0.7139 (tp30)
REVERT: A 4152 LYS cc_start: 0.8049 (pptt) cc_final: 0.7627 (pptt)
REVERT: A 4174 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6531 (pt0)
REVERT: A 4176 LEU cc_start: 0.5403 (OUTLIER) cc_final: 0.4283 (mt)
  outliers start: 24
  outliers final: 15
  residues processed: 119
  average time/residue: 0.0900
  time to fit residues: 13.6317
Evaluate side-chains
  127 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
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  280 ASP
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 1582 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 4189 GLU
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 42 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 45 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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**
** A4183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.180119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.154005 restraints weight = 12400.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.158513 restraints weight = 8218.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.161994 restraints weight = 5969.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.164433 restraints weight = 4555.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.166381 restraints weight = 3646.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5997
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   6012  Z= 0.219
  Angle     :  0.717  10.784   8151  Z= 0.354
  Chirality :  0.045   0.182    892
  Planarity :  0.005   0.051   1048
  Dihedral  :  9.781 151.160    846
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 19.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 15.25 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.31), residues: 733
  helix:  0.60 (0.28), residues: 329
  sheet: -0.40 (0.52), residues: 89
  loop : -0.58 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A2843 
 TYR   0.021   0.002   TYR A 286 
 PHE   0.016   0.002   PHE A 399 
 TRP   0.026   0.002   TRP A1638 
 HIS   0.008   0.002   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 6006)
  covalent geometry    : angle       0.71249 ( 8148)
  hydrogen bonds       : bond        0.04602 (  291)
  hydrogen bonds       : angle       5.48756 (  819)
  metal coordination   : bond        0.02819 (    6)
  metal coordination   : angle       4.39930 (    3)

*********************** 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
  139 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.3041 (mm-30)
REVERT: A   28 SER cc_start: 0.7638 (t) cc_final: 0.6883 (t)
REVERT: A   32 GLU cc_start: 0.7693 (mt-10) cc_final: 0.6902 (mt-10)
REVERT: A   49 HIS cc_start: 0.7994 (m90) cc_final: 0.7709 (m90)
REVERT: A   97 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5198 (mp)
REVERT: A  164 LEU cc_start: 0.7564 (mt) cc_final: 0.7126 (tt)
REVERT: A  400 TRP cc_start: 0.7365 (m-10) cc_final: 0.6958 (m-10)
REVERT: A  422 ARG cc_start: 0.7335 (tpm170) cc_final: 0.6866 (tpm170)
REVERT: A  449 GLU cc_start: 0.6002 (tp30) cc_final: 0.5742 (tp30)
REVERT: A  458 TYR cc_start: 0.7158 (m-80) cc_final: 0.6900 (m-80)
REVERT: A 1582 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7159 (pp)
REVERT: A 1615 TYR cc_start: 0.8243 (t80) cc_final: 0.7734 (t80)
REVERT: A 1644 GLU cc_start: 0.5730 (tp30) cc_final: 0.5381 (tm-30)
REVERT: A 4152 LYS cc_start: 0.8153 (pptt) cc_final: 0.7783 (pptt)
REVERT: A 4174 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6529 (pt0)
REVERT: A 4191 GLU cc_start: 0.8628 (pp20) cc_final: 0.8317 (pp20)
  outliers start: 29
  outliers final: 18
  residues processed: 128
  average time/residue: 0.0836
  time to fit residues: 13.7578
Evaluate side-chains
  129 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   86 LYS
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  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 1582 LEU
Chi-restraints excluded: chain A residue 1585 CYS
Chi-restraints excluded: chain A residue 1586 GLN
Chi-restraints excluded: chain A residue 1589 THR
Chi-restraints excluded: chain A residue 1636 THR
Chi-restraints excluded: chain A residue 1658 VAL
Chi-restraints excluded: chain A residue 2837 HIS
Chi-restraints excluded: chain A residue 4131 THR
Chi-restraints excluded: chain A residue 4174 GLN
Chi-restraints excluded: chain A residue 4189 GLU
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 48 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 19 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 6 optimal weight:    0.3980
   chunk 22 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   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 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
A 358 GLN
** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2859 HIS
** A4183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.184705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.158394 restraints weight = 11878.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.163052 restraints weight = 7822.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.166384 restraints weight = 5593.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.168989 restraints weight = 4251.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.170797 restraints weight = 3345.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.4370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5907
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6012  Z= 0.137
  Angle     :  0.669  11.086   8151  Z= 0.326
  Chirality :  0.044   0.250    892
  Planarity :  0.005   0.049   1048
  Dihedral  :  9.617 152.290    846
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 16.89 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.31), residues: 733
  helix:  0.81 (0.28), residues: 331
  sheet: -0.05 (0.52), residues: 85
  loop : -0.60 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A2843 
 TYR   0.014   0.002   TYR A 286 
 PHE   0.010   0.001   PHE A 399 
 TRP   0.026   0.001   TRP A1638 
 HIS   0.005   0.001   HIS A2884 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6006)
  covalent geometry    : angle       0.66580 ( 8148)
  hydrogen bonds       : bond        0.04081 (  291)
  hydrogen bonds       : angle       5.21082 (  819)
  metal coordination   : bond        0.02942 (    6)
  metal coordination   : angle       3.25625 (    3)

*********************** 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
  139 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.3357 (mm-30)
REVERT: A   28 SER cc_start: 0.7649 (t) cc_final: 0.6853 (t)
REVERT: A   32 GLU cc_start: 0.7657 (mt-10) cc_final: 0.6919 (mt-10)
REVERT: A   40 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7482 (tm-30)
REVERT: A   49 HIS cc_start: 0.7972 (m90) cc_final: 0.7661 (m90)
REVERT: A   97 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5327 (mp)
REVERT: A  164 LEU cc_start: 0.7521 (mt) cc_final: 0.7045 (tt)
REVERT: A  353 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7317 (tp-100)
REVERT: A  400 TRP cc_start: 0.7276 (m-10) cc_final: 0.6926 (m-10)
REVERT: A  422 ARG cc_start: 0.7267 (tpm170) cc_final: 0.6892 (tpm170)
REVERT: A  433 LEU cc_start: 0.6049 (mp) cc_final: 0.5348 (mt)
REVERT: A  449 GLU cc_start: 0.5710 (tp30) cc_final: 0.5448 (tp30)
REVERT: A  458 TYR cc_start: 0.7059 (m-10) cc_final: 0.6285 (m-80)
REVERT: A 1582 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6789 (pp)
REVERT: A 1586 GLN cc_start: 0.6375 (OUTLIER) cc_final: 0.6042 (mm-40)
REVERT: A 1615 TYR cc_start: 0.8066 (t80) cc_final: 0.7518 (t80)
REVERT: A 1644 GLU cc_start: 0.5389 (tp30) cc_final: 0.5023 (tm-30)
REVERT: A 2836 GLU cc_start: 0.7291 (tp30) cc_final: 0.7034 (tp30)
REVERT: A 4152 LYS cc_start: 0.8094 (pptt) cc_final: 0.7747 (pptt)
REVERT: A 4174 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6667 (pt0)
REVERT: A 4176 LEU cc_start: 0.5550 (OUTLIER) cc_final: 0.4377 (mt)
REVERT: A 4191 GLU cc_start: 0.8612 (pp20) cc_final: 0.8271 (pp20)
  outliers start: 27
  outliers final: 15
  residues processed: 126
  average time/residue: 0.0802
  time to fit residues: 13.0475
Evaluate side-chains
  130 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
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  273 LEU
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  353 GLN
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  483 TYR
Chi-restraints excluded: chain A residue 1582 LEU
Chi-restraints excluded: chain A residue 1585 CYS
Chi-restraints excluded: chain A residue 1586 GLN
Chi-restraints excluded: chain A residue 1589 THR
Chi-restraints excluded: chain A residue 1658 VAL
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 4189 GLU
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 68 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 70 optimal weight:    0.0670
   chunk 58 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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 154 HIS ** 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 = 0.4550 r_free = 0.4550 target = 0.185403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.159088 restraints weight = 11953.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.163752 restraints weight = 7816.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.167218 restraints weight = 5571.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.169753 restraints weight = 4193.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.171622 restraints weight = 3305.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.4375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5888
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6012  Z= 0.131
  Angle     :  0.652  11.407   8151  Z= 0.317
  Chirality :  0.043   0.229    892
  Planarity :  0.005   0.047   1048
  Dihedral  :  9.520 153.111    846
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 18.85 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.31), residues: 733
  helix:  0.90 (0.28), residues: 331
  sheet: -0.01 (0.53), residues: 85
  loop : -0.59 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2843 
 TYR   0.024   0.002   TYR A 265 
 PHE   0.010   0.001   PHE A 399 
 TRP   0.029   0.001   TRP A1638 
 HIS   0.004   0.001   HIS A2884 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6006)
  covalent geometry    : angle       0.64936 ( 8148)
  hydrogen bonds       : bond        0.03914 (  291)
  hydrogen bonds       : angle       5.08235 (  819)
  metal coordination   : bond        0.02543 (    6)
  metal coordination   : angle       3.06092 (    3)

*********************** 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
  134 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.3227 (mm-30)
REVERT: A   28 SER cc_start: 0.7684 (t) cc_final: 0.6906 (t)
REVERT: A   32 GLU cc_start: 0.7689 (mt-10) cc_final: 0.6946 (mt-10)
REVERT: A   40 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7430 (tm-30)
REVERT: A   49 HIS cc_start: 0.7921 (m90) cc_final: 0.7655 (m90)
REVERT: A  353 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7307 (tp-100)
REVERT: A  400 TRP cc_start: 0.7310 (m-10) cc_final: 0.6952 (m-10)
REVERT: A  422 ARG cc_start: 0.7269 (tpm170) cc_final: 0.6883 (tpm170)
REVERT: A  433 LEU cc_start: 0.5927 (mp) cc_final: 0.5249 (mt)
REVERT: A  449 GLU cc_start: 0.5780 (tp30) cc_final: 0.5479 (tp30)
REVERT: A 1582 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6869 (pp)
REVERT: A 1586 GLN cc_start: 0.6476 (OUTLIER) cc_final: 0.6201 (mm-40)
REVERT: A 1615 TYR cc_start: 0.8098 (t80) cc_final: 0.7541 (t80)
REVERT: A 1644 GLU cc_start: 0.5385 (tp30) cc_final: 0.5048 (tm-30)
REVERT: A 2836 GLU cc_start: 0.7340 (tp30) cc_final: 0.7068 (tp30)
REVERT: A 4152 LYS cc_start: 0.8103 (pptt) cc_final: 0.7748 (pptt)
REVERT: A 4176 LEU cc_start: 0.5528 (OUTLIER) cc_final: 0.4391 (mt)
REVERT: A 4191 GLU cc_start: 0.8633 (pp20) cc_final: 0.8228 (pp20)
  outliers start: 23
  outliers final: 15
  residues processed: 123
  average time/residue: 0.0868
  time to fit residues: 13.7351
Evaluate side-chains
  131 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
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  273 LEU
Chi-restraints excluded: chain A residue  322 SER
Chi-restraints excluded: chain A residue  353 GLN
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue  483 TYR
Chi-restraints excluded: chain A residue 1582 LEU
Chi-restraints excluded: chain A residue 1585 CYS
Chi-restraints excluded: chain A residue 1586 GLN
Chi-restraints excluded: chain A residue 1589 THR
Chi-restraints excluded: chain A residue 1658 VAL
Chi-restraints excluded: chain A residue 2837 HIS
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 38 optimal weight:    0.0970
   chunk 25 optimal weight:    0.0070
   chunk 30 optimal weight:    0.8980
   chunk 7 optimal weight:    0.3980
   chunk 18 optimal weight:    0.0470
   chunk 53 optimal weight:    0.0870
   chunk 14 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.1272

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

Flipped N/Q/H residues before XYZ refinement:
A  11 HIS
** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1588 GLN
** A1673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A4174 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.187969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.161495 restraints weight = 11840.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.166287 restraints weight = 7744.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.169773 restraints weight = 5510.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.172375 restraints weight = 4152.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.174201 restraints weight = 3263.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.4406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5824
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6012  Z= 0.120
  Angle     :  0.656  12.197   8151  Z= 0.318
  Chirality :  0.043   0.220    892
  Planarity :  0.004   0.046   1048
  Dihedral  :  9.475 151.548    846
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 19.34 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.32), residues: 733
  helix:  0.99 (0.28), residues: 330
  sheet: -0.05 (0.53), residues: 87
  loop : -0.44 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 465 
 TYR   0.016   0.001   TYR A2839 
 PHE   0.009   0.001   PHE A 399 
 TRP   0.030   0.001   TRP A1638 
 HIS   0.003   0.001   HIS A2884 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6006)
  covalent geometry    : angle       0.65437 ( 8148)
  hydrogen bonds       : bond        0.03711 (  291)
  hydrogen bonds       : angle       4.89810 (  819)
  metal coordination   : bond        0.02535 (    6)
  metal coordination   : angle       2.72557 (    3)

*********************** 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
  139 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.3114 (mm-30)
REVERT: A   28 SER cc_start: 0.7668 (t) cc_final: 0.6903 (t)
REVERT: A   32 GLU cc_start: 0.7633 (mt-10) cc_final: 0.6902 (mt-10)
REVERT: A   40 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7395 (tm-30)
REVERT: A   49 HIS cc_start: 0.7858 (m90) cc_final: 0.7567 (m90)
REVERT: A  400 TRP cc_start: 0.7262 (m-10) cc_final: 0.6904 (m-10)
REVERT: A  422 ARG cc_start: 0.7230 (tpm170) cc_final: 0.6891 (tpm170)
REVERT: A  433 LEU cc_start: 0.5731 (mp) cc_final: 0.5032 (mt)
REVERT: A 1582 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6865 (pp)
REVERT: A 1586 GLN cc_start: 0.6388 (OUTLIER) cc_final: 0.6135 (mm-40)
REVERT: A 1588 GLN cc_start: 0.6202 (OUTLIER) cc_final: 0.5127 (mp-120)
REVERT: A 1615 TYR cc_start: 0.8032 (t80) cc_final: 0.7474 (t80)
REVERT: A 1616 ARG cc_start: 0.7727 (ttt-90) cc_final: 0.7078 (ttt-90)
REVERT: A 1644 GLU cc_start: 0.5127 (tp30) cc_final: 0.4880 (tm-30)
REVERT: A 2836 GLU cc_start: 0.7219 (tp30) cc_final: 0.6932 (tp30)
REVERT: A 4152 LYS cc_start: 0.8080 (pptt) cc_final: 0.7706 (pptt)
REVERT: A 4176 LEU cc_start: 0.5422 (OUTLIER) cc_final: 0.4293 (mt)
REVERT: A 4191 GLU cc_start: 0.8610 (pp20) cc_final: 0.8201 (pp20)
  outliers start: 23
  outliers final: 13
  residues processed: 129
  average time/residue: 0.0913
  time to fit residues: 14.9143
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  : 0.204 
-------------------------------------------------------------------------------
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  258 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue 1582 LEU
Chi-restraints excluded: chain A residue 1586 GLN
Chi-restraints excluded: chain A residue 1588 GLN
Chi-restraints excluded: chain A residue 1589 THR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0170
   chunk 53 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 48 optimal weight:    0.2980
   chunk 18 optimal weight:    9.9990
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 HIS ** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.187188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.160793 restraints weight = 12042.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.165576 restraints weight = 7835.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.169087 restraints weight = 5556.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.171697 restraints weight = 4167.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.173639 restraints weight = 3264.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.4401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5840
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6012  Z= 0.124
  Angle     :  0.666  12.298   8151  Z= 0.322
  Chirality :  0.043   0.222    892
  Planarity :  0.004   0.046   1048
  Dihedral  :  9.406 152.205    846
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 20.82 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.31), residues: 733
  helix:  1.01 (0.29), residues: 329
  sheet: -0.02 (0.54), residues: 87
  loop : -0.48 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A4134 
 TYR   0.014   0.001   TYR A2839 
 PHE   0.010   0.001   PHE A 211 
 TRP   0.032   0.001   TRP A1638 
 HIS   0.005   0.001   HIS A1675 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6006)
  covalent geometry    : angle       0.66361 ( 8148)
  hydrogen bonds       : bond        0.03631 (  291)
  hydrogen bonds       : angle       4.87579 (  819)
  metal coordination   : bond        0.02233 (    6)
  metal coordination   : angle       2.79511 (    3)

*********************** 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
  129 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.3003 (mm-30)
REVERT: A   28 SER cc_start: 0.7675 (t) cc_final: 0.6904 (t)
REVERT: A   32 GLU cc_start: 0.7632 (mt-10) cc_final: 0.6901 (mt-10)
REVERT: A   40 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7390 (tm-30)
REVERT: A  400 TRP cc_start: 0.7338 (m-10) cc_final: 0.6965 (m-10)
REVERT: A  422 ARG cc_start: 0.7230 (tpm170) cc_final: 0.6894 (tpm170)
REVERT: A  431 GLU cc_start: 0.7964 (pm20) cc_final: 0.7747 (pm20)
REVERT: A  433 LEU cc_start: 0.5737 (mp) cc_final: 0.5026 (mt)
REVERT: A 1615 TYR cc_start: 0.8044 (t80) cc_final: 0.7493 (t80)
REVERT: A 1616 ARG cc_start: 0.7726 (ttt-90) cc_final: 0.7267 (ttt-90)
REVERT: A 1644 GLU cc_start: 0.5118 (tp30) cc_final: 0.4853 (tm-30)
REVERT: A 4152 LYS cc_start: 0.8084 (pptt) cc_final: 0.7709 (pptt)
REVERT: A 4176 LEU cc_start: 0.5494 (OUTLIER) cc_final: 0.4366 (mt)
REVERT: A 4191 GLU cc_start: 0.8614 (pp20) cc_final: 0.8190 (pp20)
  outliers start: 18
  outliers final: 12
  residues processed: 122
  average time/residue: 0.0889
  time to fit residues: 13.8975
Evaluate side-chains
  123 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
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  258 ILE
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue 1589 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 33 optimal weight:    0.0870
   chunk 7 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0370
   chunk 0 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.5836

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
** 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 = 0.4563 r_free = 0.4563 target = 0.186675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.159986 restraints weight = 12062.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.164821 restraints weight = 7826.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.168287 restraints weight = 5541.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.170758 restraints weight = 4156.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.172766 restraints weight = 3280.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.4390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5858
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6012  Z= 0.129
  Angle     :  0.680  12.794   8151  Z= 0.328
  Chirality :  0.042   0.221    892
  Planarity :  0.004   0.046   1048
  Dihedral  :  9.379 153.015    846
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.98 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.31), residues: 733
  helix:  0.97 (0.29), residues: 334
  sheet: -0.09 (0.53), residues: 89
  loop : -0.49 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A4134 
 TYR   0.012   0.001   TYR A2839 
 PHE   0.012   0.001   PHE A 211 
 TRP   0.033   0.001   TRP A1638 
 HIS   0.003   0.001   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6006)
  covalent geometry    : angle       0.67804 ( 8148)
  hydrogen bonds       : bond        0.03672 (  291)
  hydrogen bonds       : angle       4.88214 (  819)
  metal coordination   : bond        0.02109 (    6)
  metal coordination   : angle       2.84568 (    3)

********************** 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
  127 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.2982 (mm-30)
REVERT: A   28 SER cc_start: 0.7640 (t) cc_final: 0.6870 (t)
REVERT: A   32 GLU cc_start: 0.7637 (mt-10) cc_final: 0.6882 (mt-10)
REVERT: A   40 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7333 (tm-30)
REVERT: A  400 TRP cc_start: 0.7455 (m-10) cc_final: 0.7061 (m-10)
REVERT: A  421 LYS cc_start: 0.7501 (pptt) cc_final: 0.7203 (tttt)
REVERT: A  422 ARG cc_start: 0.7238 (tpm170) cc_final: 0.6803 (tpm170)
REVERT: A  431 GLU cc_start: 0.7953 (pm20) cc_final: 0.7743 (pm20)
REVERT: A  433 LEU cc_start: 0.5820 (mp) cc_final: 0.5113 (mt)
REVERT: A  449 GLU cc_start: 0.5958 (tp30) cc_final: 0.5728 (tp30)
REVERT: A 1615 TYR cc_start: 0.8055 (t80) cc_final: 0.7513 (t80)
REVERT: A 1616 ARG cc_start: 0.7691 (ttt-90) cc_final: 0.7244 (ttt-90)
REVERT: A 1644 GLU cc_start: 0.5145 (tp30) cc_final: 0.4920 (tm-30)
REVERT: A 4152 LYS cc_start: 0.8089 (pptt) cc_final: 0.7736 (pptt)
REVERT: A 4191 GLU cc_start: 0.8642 (pp20) cc_final: 0.8208 (pp20)
  outliers start: 15
  outliers final: 13
  residues processed: 121
  average time/residue: 0.0843
  time to fit residues: 13.1085
Evaluate side-chains
  124 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
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  258 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  464 THR
Chi-restraints excluded: chain A residue 1658 VAL
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 71 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0370
   chunk 49 optimal weight:    0.6980
   chunk 72 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0870
   overall best weight:    0.4036

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
** 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 = 0.4575 r_free = 0.4575 target = 0.187694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.161026 restraints weight = 11845.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.165823 restraints weight = 7720.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.169328 restraints weight = 5488.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.171924 restraints weight = 4129.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.173772 restraints weight = 3247.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.4401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5828
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6012  Z= 0.123
  Angle     :  0.686  12.797   8151  Z= 0.332
  Chirality :  0.043   0.220    892
  Planarity :  0.004   0.052   1048
  Dihedral  :  9.350 152.442    846
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 21.80 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.32), residues: 733
  helix:  1.04 (0.29), residues: 335
  sheet: -0.06 (0.53), residues: 89
  loop : -0.46 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A4134 
 TYR   0.012   0.001   TYR A2839 
 PHE   0.013   0.001   PHE A 211 
 TRP   0.031   0.001   TRP A1638 
 HIS   0.003   0.001   HIS A2884 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6006)
  covalent geometry    : angle       0.68393 ( 8148)
  hydrogen bonds       : bond        0.03549 (  291)
  hydrogen bonds       : angle       4.79014 (  819)
  metal coordination   : bond        0.02148 (    6)
  metal coordination   : angle       2.73453 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1129.76 seconds
wall clock time: 20 minutes 14.53 seconds (1214.53 seconds total)