Starting phenix.real_space_refine
on Wed Jun 18 00:02:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6h3i_0133/06_2025/6h3i_0133.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6h3i_0133/06_2025/6h3i_0133.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6h3i_0133/06_2025/6h3i_0133.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6h3i_0133/06_2025/6h3i_0133.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6h3i_0133/06_2025/6h3i_0133.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6h3i_0133/06_2025/6h3i_0133.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.014
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: 5
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C   12990      2.51       5
     N    3461      2.21       5
     O    4049      1.98       5
     H      53      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 20599
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 16848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2124, 16848
          Classifications: {'peptide': 2124}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 97, 'TRANS': 2026}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 1043
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 1043
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 2708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 345, 2708
          Classifications: {'peptide': 345}
          Link IDs: {'PTRANS': 13, 'TRANS': 331}
          Chain breaks: 4
  Time building chain proxies: 12.28, per 1000 atoms: 0.60
  Number of scatterers: 20599
  At special positions: 0
  Unit cell: (117.26, 127.1, 135.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      46     16.00
     O    4049      8.00
     N    3461      7.00
     C   12990      6.00
     H      53      1.00
    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: 4.93
  Conformation dependent library (CDL) restraints added in 2.7 seconds
  

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4816

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 0 sheets defined
      10.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 182 through 186
      removed outlier: 3.906A  pdb=" N   THR A 185 " --> pdb=" O   LYS A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 306
      removed outlier: 4.398A  pdb=" N   ASP A 303 " --> pdb=" O   ARG A 299 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   VAL A 304 " --> pdb=" O   ASN A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 363
      removed outlier: 3.709A  pdb=" N   GLU A 362 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 386
      removed outlier: 4.261A  pdb=" N   ASN A 386 " --> pdb=" O   ASN A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 413
      removed outlier: 3.533A  pdb=" N   GLY A 413 " --> pdb=" O   ALA A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 523
      removed outlier: 3.869A  pdb=" N   ASN A 521 " --> pdb=" O   ASN A 517 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   MET A 523 " --> pdb=" O   VAL A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 583
    Processing helix  chain 'A' and resid 627 through 634
    Processing helix  chain 'A' and resid 656 through 660
      removed outlier: 3.686A  pdb=" N   MET A 659 " --> pdb=" O   PHE A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 735
      removed outlier: 3.534A  pdb=" N   ALA A 735 " --> pdb=" O   PRO A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 819
    Processing helix  chain 'A' and resid 845 through 849
    Processing helix  chain 'A' and resid 914 through 920
      removed outlier: 4.306A  pdb=" N   TYR A 918 " --> pdb=" O   ASP A 914 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 944
      removed outlier: 3.896A  pdb=" N   LEU A 943 " --> pdb=" O   TYR A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 986
      removed outlier: 3.547A  pdb=" N   ASN A 986 " --> pdb=" O   PRO A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1003
    Processing helix  chain 'A' and resid 1081 through 1089
      removed outlier: 4.267A  pdb=" N   ASN A1087 " --> pdb=" O   ASP A1083 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1132
      removed outlier: 4.272A  pdb=" N   TYR A1132 " --> pdb=" O   VAL A1128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1412 through 1417
    Processing helix  chain 'A' and resid 1426 through 1439
      removed outlier: 3.995A  pdb=" N   LEU A1430 " --> pdb=" O   ALA A1426 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR A1431 " --> pdb=" O   LEU A1427 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ARG A1432 " --> pdb=" O   ASP A1428 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   SER A1439 " --> pdb=" O   ILE A1435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1571 through 1576
    Processing helix  chain 'A' and resid 1607 through 1613
    Processing helix  chain 'A' and resid 1617 through 1622
    Processing helix  chain 'A' and resid 1856 through 1861
      removed outlier: 3.647A  pdb=" N   SER A1860 " --> pdb=" O   SER A1856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1978 through 1982
    Processing helix  chain 'A' and resid 1989 through 1995
      removed outlier: 3.705A  pdb=" N   GLY A1995 " --> pdb=" O   ALA A1991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2072 through 2076
      removed outlier: 4.214A  pdb=" N   PHE A2076 " --> pdb=" O   LYS A2073 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2084 through 2104
      removed outlier: 3.965A  pdb=" N   ARG A2094 " --> pdb=" O   PHE A2090 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   LEU A2095 " --> pdb=" O   ARG A2091 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ILE A2096 " --> pdb=" O   SER A2092 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2107 through 2111
      removed outlier: 3.521A  pdb=" N   VAL A2110 " --> pdb=" O   GLY A2107 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   ALA A2111 " --> pdb=" O   SER A2108 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2107 through 2111'
    Processing helix  chain 'A' and resid 2129 through 2135
    Processing helix  chain 'A' and resid 2147 through 2152
      removed outlier: 3.528A  pdb=" N   LEU A2151 " --> pdb=" O   ASN A2147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2152 through 2161
    Processing helix  chain 'B' and resid 27 through 42
    Processing helix  chain 'B' and resid 126 through 133
    Processing helix  chain 'F' and resid 61 through 66
    Processing helix  chain 'F' and resid 286 through 297
      removed outlier: 4.225A  pdb=" N   TYR F 292 " --> pdb=" O   ASP F 288 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 299 through 307
      removed outlier: 3.764A  pdb=" N   PHE F 305 " --> pdb=" O   VAL F 301 " (cutoff:3.500A)

    114 hydrogen bonds defined for protein.
    291 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: 4.12

  Time building geometry restraints manager: 5.81 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 53
        1.03 -     1.23: 244
        1.23 -     1.42: 8887
        1.42 -     1.62: 11763
        1.62 -     1.81: 90
  Bond restraints: 21037
  Sorted by residual:
  bond pdb=" CD2 TYR A 309 "
       pdb=" CE2 TYR A 309 "
    ideal  model  delta    sigma   weight residual
    1.382  1.310  0.072 3.00e-02 1.11e+03 5.83e+00
  bond pdb=" CB  TYR A 309 "
       pdb=" CG  TYR A 309 "
    ideal  model  delta    sigma   weight residual
    1.512  1.467  0.045 2.20e-02 2.07e+03 4.10e+00
  bond pdb=" C   ASP A1600 "
       pdb=" N   PRO A1601 "
    ideal  model  delta    sigma   weight residual
    1.334  1.288  0.046 2.34e-02 1.83e+03 3.88e+00
  bond pdb=" CB  ILE A 990 "
       pdb=" CG2 ILE A 990 "
    ideal  model  delta    sigma   weight residual
    1.521  1.456  0.065 3.30e-02 9.18e+02 3.83e+00
  bond pdb=" CB  VAL A1345 "
       pdb=" CG1 VAL A1345 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.37e+00
  ... (remaining 21032 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 27821
        2.50 -     5.00: 659
        5.00 -     7.51: 69
        7.51 -    10.01: 8
       10.01 -    12.51: 1
  Bond angle restraints: 28558
  Sorted by residual:
  angle pdb=" N   GLN F  58 "
        pdb=" CA  GLN F  58 "
        pdb=" C   GLN F  58 "
      ideal   model   delta    sigma   weight residual
     114.04  107.91    6.13 1.24e+00 6.50e-01 2.44e+01
  angle pdb=" C   GLU A1035 "
        pdb=" N   ILE A1036 "
        pdb=" CA  ILE A1036 "
      ideal   model   delta    sigma   weight residual
     120.49  126.64   -6.15 1.38e+00 5.25e-01 1.99e+01
  angle pdb=" N   ASN A 822 "
        pdb=" CA  ASN A 822 "
        pdb=" C   ASN A 822 "
      ideal   model   delta    sigma   weight residual
     110.80  118.76   -7.96 2.13e+00 2.20e-01 1.40e+01
  angle pdb=" N   GLY F  43 "
        pdb=" CA  GLY F  43 "
        pdb=" C   GLY F  43 "
      ideal   model   delta    sigma   weight residual
     115.46  109.67    5.79 1.63e+00 3.76e-01 1.26e+01
  angle pdb=" CA  TYR F 330 "
        pdb=" CB  TYR F 330 "
        pdb=" CG  TYR F 330 "
      ideal   model   delta    sigma   weight residual
     113.90  107.51    6.39 1.80e+00 3.09e-01 1.26e+01
  ... (remaining 28553 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.29: 11771
       15.29 -    30.58: 639
       30.58 -    45.87: 81
       45.87 -    61.17: 3
       61.17 -    76.46: 19
  Dihedral angle restraints: 12513
    sinusoidal: 4972
      harmonic: 7541
  Sorted by residual:
  dihedral pdb=" CA  GLN A 501 "
           pdb=" C   GLN A 501 "
           pdb=" N   SER A 502 "
           pdb=" CA  SER A 502 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.73  -30.27     0      5.00e+00 4.00e-02 3.67e+01
  dihedral pdb=" CA  GLN A1563 "
           pdb=" C   GLN A1563 "
           pdb=" N   TYR A1564 "
           pdb=" CA  TYR A1564 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.89   30.11     0      5.00e+00 4.00e-02 3.63e+01
  dihedral pdb=" CA  ASN A 308 "
           pdb=" C   ASN A 308 "
           pdb=" N   TYR A 309 "
           pdb=" CA  TYR A 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.00  -30.00     0      5.00e+00 4.00e-02 3.60e+01
  ... (remaining 12510 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 2027
       0.049 -    0.098: 811
       0.098 -    0.147: 241
       0.147 -    0.196: 13
       0.196 -    0.245: 2
  Chirality restraints: 3094
  Sorted by residual:
  chirality pdb=" CA  ASN A 998 "
            pdb=" N   ASN A 998 "
            pdb=" C   ASN A 998 "
            pdb=" CB  ASN A 998 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  PRO A2178 "
            pdb=" N   PRO A2178 "
            pdb=" C   PRO A2178 "
            pdb=" CB  PRO A2178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  TYR F 330 "
            pdb=" N   TYR F 330 "
            pdb=" C   TYR F 330 "
            pdb=" CB  TYR F 330 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.42e-01
  ... (remaining 3091 not shown)

  Planarity restraints: 3766
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A2250 "    0.048 5.00e-02 4.00e+02   7.13e-02 8.14e+00
        pdb=" N   PRO A2251 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A2251 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A2251 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 129 "    0.022 2.00e-02 2.50e+03   1.60e-02 7.05e+00
        pdb=" CG  TRP B 129 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 129 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 129 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 129 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 129 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 129 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 129 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 129 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 129 "    0.002 2.00e-02 2.50e+03
        pdb=" HE1 TRP B 129 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A2177 "   -0.042 5.00e-02 4.00e+02   6.38e-02 6.50e+00
        pdb=" N   PRO A2178 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A2178 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A2178 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 3763 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.53: 223
        2.53 -     3.05: 15822
        3.05 -     3.56: 22878
        3.56 -     4.08: 36865
        4.08 -     4.60: 53899
  Nonbonded interactions: 129687
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 101 "
            pdb=" HH  TYR B 120 "
     model   vdw
     2.010 2.450
  nonbonded pdb=" OD1 ASP A2030 "
            pdb=" OG  SER A2181 "
     model   vdw
     2.012 2.800
  nonbonded pdb=" OG1 THR A1847 "
            pdb=" OG  SER A1881 "
     model   vdw
     2.014 2.800
  nonbonded pdb=" O   GLN A1338 "
            pdb=" OG  SER A1492 "
     model   vdw
     2.024 2.800
  nonbonded pdb=" O   LEU F 146 "
            pdb=" OG  SER F 153 "
     model   vdw
     2.043 2.800
  ... (remaining 129682 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             2.100
  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:             0.560
  Extract box with map and model:          0.840
  Check model and map are aligned:         0.150
  Set scattering table:                    0.180
  Process input model:                     43.010
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
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      :  0.009   0.072  20984  Z= 0.403
  Angle     :  0.921  12.509  28466  Z= 0.502
  Chirality :  0.054   0.245   3094
  Planarity :  0.006   0.071   3766
  Dihedral  : 10.079  76.457   7671
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 39.59
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 21.41 %
    Favored  : 78.43 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  3.41 %
    Favored  : 96.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.64 (0.13), residues: 2559
  helix: -3.64 (0.20), residues: 251
  sheet: -3.59 (0.15), residues: 898
  loop : -3.96 (0.14), residues: 1410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.004   TRP B 129 
 HIS   0.009   0.002   HIS A1672 
 PHE   0.039   0.003   PHE A 656 
 TYR   0.039   0.003   TYR A1120 
 ARG   0.010   0.001   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18063 (  114)
  hydrogen bonds       : angle       6.17576 (  291)
  covalent geometry    : bond        0.00922 (20984)
  covalent geometry    : angle       0.92098 (28466)

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

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

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 226
  time to evaluate  : 2.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  728 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.9030 (pp)
REVERT: A  749 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7758 (pp)
REVERT: A 1768 TYR cc_start: 0.7667 (m-80) cc_final: 0.7300 (m-10)
REVERT: A 2209 SER cc_start: 0.9300 (p) cc_final: 0.9025 (m)
REVERT: A 2257 PHE cc_start: 0.7735 (t80) cc_final: 0.7492 (t80)
REVERT: B  112 ASP cc_start: 0.8183 (t70) cc_final: 0.7937 (t70)
REVERT: B  141 GLU cc_start: 0.7544 (tt0) cc_final: 0.7167 (tt0)
REVERT: B  142 ILE cc_start: 0.9373 (tt) cc_final: 0.9150 (tt)
  outliers start: 9
  outliers final: 1
  residues processed: 234
  average time/residue: 0.3846
  time to fit residues: 137.0683
Evaluate side-chains
  125 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 122
  time to evaluate  : 2.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  962 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 217 optimal weight:    7.9990
   chunk 195 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9990
   chunk 66 optimal weight:    6.9990
   chunk 131 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 202 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 150 optimal weight:    6.9990
   chunk 234 optimal weight:   10.0000
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 865 GLN
** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1190 ASN
** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1551 GLN
** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1742 GLN
** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2120 ASN
A2236 ASN
B  47 GLN
** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.077035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.065263 restraints weight = 55116.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.066689 restraints weight = 30785.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.067567 restraints weight = 22813.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  20984  Z= 0.124
  Angle     :  0.544  12.032  28466  Z= 0.286
  Chirality :  0.042   0.142   3094
  Planarity :  0.004   0.045   3766
  Dihedral  :  5.907  44.192   2842
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 48.09
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 16.73 %
    Favored  : 83.20 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  7.13 %
    Favored  : 91.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.07 (0.14), residues: 2559
  helix: -2.81 (0.26), residues: 252
  sheet: -3.27 (0.15), residues: 882
  loop : -3.62 (0.15), residues: 1425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1996 
 HIS   0.004   0.001   HIS A1672 
 PHE   0.014   0.001   PHE A 656 
 TYR   0.017   0.001   TYR A1120 
 ARG   0.003   0.001   ARG F  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03442 (  114)
  hydrogen bonds       : angle       5.40983 (  291)
  covalent geometry    : bond        0.00268 (20984)
  covalent geometry    : angle       0.54374 (28466)

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

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

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 2.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  728 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8796 (pp)
REVERT: A  749 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7662 (pp)
REVERT: A 1425 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9034 (tm)
REVERT: B   25 LYS cc_start: 0.8481 (mtmm) cc_final: 0.8275 (mttp)
REVERT: B  112 ASP cc_start: 0.8037 (t70) cc_final: 0.7486 (t0)
REVERT: B  142 ILE cc_start: 0.9364 (tt) cc_final: 0.9158 (tt)
  outliers start: 28
  outliers final: 15
  residues processed: 169
  average time/residue: 0.3312
  time to fit residues: 90.5684
Evaluate side-chains
  127 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 2.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  990 ILE
Chi-restraints excluded: chain A residue 1409 CYS
Chi-restraints excluded: chain A residue 1425 LEU
Chi-restraints excluded: chain A residue 1579 LYS
Chi-restraints excluded: chain A residue 2030 ASP
Chi-restraints excluded: chain A residue 2187 LEU
Chi-restraints excluded: chain A residue 2277 MET
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain F residue  331 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 202 optimal weight:    9.9990
   chunk 151 optimal weight:   10.0000
   chunk 81 optimal weight:    9.9990
   chunk 88 optimal weight:    0.0170
   chunk 30 optimal weight:    2.9990
   chunk 197 optimal weight:    6.9990
   chunk 7 optimal weight:    8.9990
   chunk 55 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 161 optimal weight:   10.0000
   chunk 237 optimal weight:    9.9990
   overall best weight:    5.8026

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

Flipped N/Q/H residues before XYZ refinement:
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2213 ASN
A2244 ASN
** A2344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.072464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.060612 restraints weight = 57036.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.061895 restraints weight = 31590.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.062889 restraints weight = 23839.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048  20984  Z= 0.328
  Angle     :  0.675   9.757  28466  Z= 0.352
  Chirality :  0.046   0.168   3094
  Planarity :  0.005   0.055   3766
  Dihedral  :  6.156  44.464   2842
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 47.67
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 21.14 %
    Favored  : 78.74 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  8.42 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.08 (0.15), residues: 2559
  helix: -2.93 (0.25), residues: 259
  sheet: -3.32 (0.16), residues: 900
  loop : -3.56 (0.15), residues: 1400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A1996 
 HIS   0.005   0.002   HIS F 344 
 PHE   0.035   0.002   PHE A2257 
 TYR   0.028   0.002   TYR A1120 
 ARG   0.005   0.001   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04043 (  114)
  hydrogen bonds       : angle       5.56272 (  291)
  covalent geometry    : bond        0.00743 (20984)
  covalent geometry    : angle       0.67525 (28466)

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

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

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 111
  time to evaluate  : 2.313 
Fit side-chains
   revert: symmetry clash
REVERT: A  277 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7503 (pm20)
REVERT: A  728 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8873 (pp)
REVERT: A  749 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7515 (pp)
REVERT: B  112 ASP cc_start: 0.8123 (t70) cc_final: 0.7889 (t70)
REVERT: F  137 GLU cc_start: 0.7784 (tt0) cc_final: 0.7478 (tt0)
  outliers start: 45
  outliers final: 29
  residues processed: 147
  average time/residue: 0.3301
  time to fit residues: 78.9608
Evaluate side-chains
  138 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 2.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  750 PHE
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  972 TYR
Chi-restraints excluded: chain A residue  990 ILE
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1168 MET
Chi-restraints excluded: chain A residue 1349 VAL
Chi-restraints excluded: chain A residue 1425 LEU
Chi-restraints excluded: chain A residue 1806 ILE
Chi-restraints excluded: chain A residue 2030 ASP
Chi-restraints excluded: chain A residue 2183 LYS
Chi-restraints excluded: chain A residue 2184 TYR
Chi-restraints excluded: chain A residue 2187 LEU
Chi-restraints excluded: chain A residue 2277 MET
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   76 ILE
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain F residue  331 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 140 optimal weight:    9.9990
   chunk 206 optimal weight:    0.8980
   chunk 104 optimal weight:    0.6980
   chunk 142 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 55 optimal weight:    9.9990
   chunk 201 optimal weight:    0.9980
   chunk 164 optimal weight:    6.9990
   chunk 204 optimal weight:   10.0000
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2213 ASN
A2244 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.076354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.064565 restraints weight = 56330.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.066241 restraints weight = 30750.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.067378 restraints weight = 21684.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  20984  Z= 0.091
  Angle     :  0.494   9.337  28466  Z= 0.258
  Chirality :  0.041   0.145   3094
  Planarity :  0.003   0.049   3766
  Dihedral  :  5.372  49.409   2842
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 46.28
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 15.24 %
    Favored  : 84.68 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  9.48 %
    Favored  : 89.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.62 (0.15), residues: 2559
  helix: -2.40 (0.27), residues: 264
  sheet: -2.97 (0.17), residues: 861
  loop : -3.33 (0.15), residues: 1434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2180 
 HIS   0.004   0.001   HIS A1672 
 PHE   0.018   0.001   PHE A2257 
 TYR   0.010   0.001   TYR F 292 
 ARG   0.003   0.000   ARG A1484 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02587 (  114)
  hydrogen bonds       : angle       4.97276 (  291)
  covalent geometry    : bond        0.00202 (20984)
  covalent geometry    : angle       0.49389 (28466)

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

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

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 123
  time to evaluate  : 2.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  728 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8878 (pp)
REVERT: A  749 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7502 (pp)
REVERT: A 1425 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9053 (tm)
  outliers start: 34
  outliers final: 18
  residues processed: 151
  average time/residue: 0.3009
  time to fit residues: 75.3631
Evaluate side-chains
  132 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 2.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1425 LEU
Chi-restraints excluded: chain A residue 1874 ASN
Chi-restraints excluded: chain A residue 2184 TYR
Chi-restraints excluded: chain A residue 2187 LEU
Chi-restraints excluded: chain A residue 2277 MET
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   76 ILE
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain F residue  331 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 255 optimal weight:    9.9990
   chunk 178 optimal weight:    6.9990
   chunk 191 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 219 optimal weight:   10.0000
   chunk 172 optimal weight:   10.0000
   chunk 189 optimal weight:    7.9990
   chunk 171 optimal weight:    9.9990
   chunk 63 optimal weight:    9.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    6.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1047 GLN
** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1123 ASN
** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1583 ASN
** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2213 ASN
A2244 ASN
** A2344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  47 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.071782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.059610 restraints weight = 58065.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.061218 restraints weight = 33746.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.061931 restraints weight = 24299.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.051  20984  Z= 0.359
  Angle     :  0.688   7.743  28466  Z= 0.359
  Chirality :  0.047   0.167   3094
  Planarity :  0.005   0.054   3766
  Dihedral  :  5.979  52.130   2842
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 49.03
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 21.84 %
    Favored  : 78.00 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  :  9.92 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.82 (0.15), residues: 2559
  helix: -2.66 (0.26), residues: 259
  sheet: -3.15 (0.16), residues: 925
  loop : -3.39 (0.15), residues: 1375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A1996 
 HIS   0.005   0.002   HIS F 344 
 PHE   0.029   0.002   PHE A2257 
 TYR   0.026   0.002   TYR A1120 
 ARG   0.006   0.001   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03878 (  114)
  hydrogen bonds       : angle       5.38687 (  291)
  covalent geometry    : bond        0.00811 (20984)
  covalent geometry    : angle       0.68828 (28466)

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

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

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 112
  time to evaluate  : 2.341 
Fit side-chains
   revert: symmetry clash
REVERT: A  277 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7448 (pm20)
REVERT: A  728 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8927 (pp)
REVERT: A  749 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7610 (pp)
REVERT: F  137 GLU cc_start: 0.7776 (tt0) cc_final: 0.7489 (tt0)
  outliers start: 67
  outliers final: 46
  residues processed: 168
  average time/residue: 0.2916
  time to fit residues: 81.4212
Evaluate side-chains
  152 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 103
  time to evaluate  : 2.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  659 MET
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  750 PHE
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain A residue  870 MET
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  972 TYR
Chi-restraints excluded: chain A residue  990 ILE
Chi-restraints excluded: chain A residue 1057 VAL
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1168 MET
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1315 TYR
Chi-restraints excluded: chain A residue 1363 LEU
Chi-restraints excluded: chain A residue 1425 LEU
Chi-restraints excluded: chain A residue 1490 VAL
Chi-restraints excluded: chain A residue 1531 ASP
Chi-restraints excluded: chain A residue 1638 ASN
Chi-restraints excluded: chain A residue 1806 ILE
Chi-restraints excluded: chain A residue 1874 ASN
Chi-restraints excluded: chain A residue 2027 LEU
Chi-restraints excluded: chain A residue 2030 ASP
Chi-restraints excluded: chain A residue 2103 GLU
Chi-restraints excluded: chain A residue 2184 TYR
Chi-restraints excluded: chain A residue 2187 LEU
Chi-restraints excluded: chain A residue 2211 THR
Chi-restraints excluded: chain A residue 2231 ASN
Chi-restraints excluded: chain A residue 2277 MET
Chi-restraints excluded: chain A residue 2370 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   76 ILE
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain F residue  331 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 255 optimal weight:    4.9990
   chunk 213 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 159 optimal weight:    0.2980
   chunk 18 optimal weight:    6.9990
   chunk 165 optimal weight:    5.9990
   chunk 172 optimal weight:    4.9990
   chunk 62 optimal weight:    9.9990
   chunk 138 optimal weight:    9.9990
   chunk 181 optimal weight:    4.9990
   overall best weight:    3.2588

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

Flipped N/Q/H residues before XYZ refinement:
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1047 GLN
** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1123 ASN
** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.073507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.061486 restraints weight = 56769.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.063147 restraints weight = 32949.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.063747 restraints weight = 23972.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  20984  Z= 0.191
  Angle     :  0.558   8.105  28466  Z= 0.291
  Chirality :  0.043   0.171   3094
  Planarity :  0.003   0.052   3766
  Dihedral  :  5.685  58.557   2842
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 46.95
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 18.21 %
    Favored  : 81.71 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.83 %
    Favored  : 86.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.58 (0.16), residues: 2559
  helix: -2.33 (0.28), residues: 251
  sheet: -2.94 (0.17), residues: 868
  loop : -3.31 (0.15), residues: 1440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1996 
 HIS   0.004   0.001   HIS A1672 
 PHE   0.029   0.001   PHE A2257 
 TYR   0.017   0.001   TYR A1120 
 ARG   0.003   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03036 (  114)
  hydrogen bonds       : angle       5.14741 (  291)
  covalent geometry    : bond        0.00431 (20984)
  covalent geometry    : angle       0.55825 (28466)

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

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

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 108
  time to evaluate  : 2.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  728 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8914 (pp)
REVERT: A  749 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7601 (pp)
REVERT: F  137 GLU cc_start: 0.7784 (tt0) cc_final: 0.7527 (tt0)
  outliers start: 40
  outliers final: 30
  residues processed: 139
  average time/residue: 0.3044
  time to fit residues: 69.5271
Evaluate side-chains
  137 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 2.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  659 MET
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  750 PHE
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  972 TYR
Chi-restraints excluded: chain A residue  990 ILE
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1168 MET
Chi-restraints excluded: chain A residue 1243 MET
Chi-restraints excluded: chain A residue 1315 TYR
Chi-restraints excluded: chain A residue 1490 VAL
Chi-restraints excluded: chain A residue 1874 ASN
Chi-restraints excluded: chain A residue 2187 LEU
Chi-restraints excluded: chain A residue 2259 LEU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   76 ILE
Chi-restraints excluded: chain F residue  130 THR
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain F residue  331 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 239 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 206 optimal weight:   10.0000
   chunk 28 optimal weight:    0.0980
   chunk 202 optimal weight:   10.0000
   chunk 209 optimal weight:    7.9990
   chunk 254 optimal weight:    9.9990
   chunk 177 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 89 optimal weight:    0.0870
   chunk 170 optimal weight:    6.9990
   overall best weight:    3.4364

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

Flipped N/Q/H residues before XYZ refinement:
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2001 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 = 0.3221 r_free = 0.3221 target = 0.073230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.061373 restraints weight = 56838.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.062688 restraints weight = 32602.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.063775 restraints weight = 24232.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  20984  Z= 0.199
  Angle     :  0.558   8.646  28466  Z= 0.290
  Chirality :  0.043   0.147   3094
  Planarity :  0.003   0.050   3766
  Dihedral  :  5.549  58.313   2842
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 46.75
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 19.77 %
    Favored  : 80.15 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 11.87 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.48 (0.16), residues: 2559
  helix: -2.25 (0.28), residues: 252
  sheet: -2.92 (0.17), residues: 886
  loop : -3.20 (0.16), residues: 1421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1996 
 HIS   0.003   0.001   HIS A1672 
 PHE   0.026   0.001   PHE A2257 
 TYR   0.016   0.001   TYR A1120 
 ARG   0.003   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03011 (  114)
  hydrogen bonds       : angle       5.08447 (  291)
  covalent geometry    : bond        0.00450 (20984)
  covalent geometry    : angle       0.55831 (28466)

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

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

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 114
  time to evaluate  : 2.415 
Fit side-chains
   revert: symmetry clash
REVERT: A  728 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8918 (pp)
REVERT: A  749 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7619 (pp)
REVERT: F  137 GLU cc_start: 0.7806 (tt0) cc_final: 0.7550 (tt0)
  outliers start: 55
  outliers final: 44
  residues processed: 153
  average time/residue: 0.3077
  time to fit residues: 80.1139
Evaluate side-chains
  155 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 109
  time to evaluate  : 2.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ASN
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  659 MET
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  750 PHE
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain A residue  870 MET
Chi-restraints excluded: chain A residue  943 LEU
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  972 TYR
Chi-restraints excluded: chain A residue  990 ILE
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1168 MET
Chi-restraints excluded: chain A residue 1243 MET
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1315 TYR
Chi-restraints excluded: chain A residue 1363 LEU
Chi-restraints excluded: chain A residue 1425 LEU
Chi-restraints excluded: chain A residue 1490 VAL
Chi-restraints excluded: chain A residue 1806 ILE
Chi-restraints excluded: chain A residue 1857 THR
Chi-restraints excluded: chain A residue 1874 ASN
Chi-restraints excluded: chain A residue 2027 LEU
Chi-restraints excluded: chain A residue 2030 ASP
Chi-restraints excluded: chain A residue 2184 TYR
Chi-restraints excluded: chain A residue 2187 LEU
Chi-restraints excluded: chain A residue 2211 THR
Chi-restraints excluded: chain A residue 2259 LEU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   76 ILE
Chi-restraints excluded: chain F residue  130 THR
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain F residue  331 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 56 optimal weight:    0.2980
   chunk 217 optimal weight:    9.9990
   chunk 210 optimal weight:    8.9990
   chunk 107 optimal weight:    0.0570
   chunk 200 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 233 optimal weight:    0.4980
   chunk 71 optimal weight:    8.9990
   chunk 126 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   chunk 144 optimal weight:    8.9990
   overall best weight:    2.5702

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

Flipped N/Q/H residues before XYZ refinement:
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1395 GLN
** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2213 ASN
A2244 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.074076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.062273 restraints weight = 56852.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.063561 restraints weight = 32244.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.064645 restraints weight = 23829.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  20984  Z= 0.153
  Angle     :  0.525   8.934  28466  Z= 0.273
  Chirality :  0.042   0.145   3094
  Planarity :  0.003   0.050   3766
  Dihedral  :  5.335  48.730   2842
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 46.13
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 17.47 %
    Favored  : 82.45 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.45 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.32 (0.16), residues: 2559
  helix: -2.06 (0.30), residues: 246
  sheet: -2.84 (0.17), residues: 877
  loop : -3.09 (0.16), residues: 1436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1996 
 HIS   0.003   0.001   HIS A1672 
 PHE   0.028   0.001   PHE A2257 
 TYR   0.014   0.001   TYR A1120 
 ARG   0.003   0.000   ARG A1484 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02740 (  114)
  hydrogen bonds       : angle       4.94031 (  291)
  covalent geometry    : bond        0.00346 (20984)
  covalent geometry    : angle       0.52543 (28466)

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

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

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 118
  time to evaluate  : 2.558 
Fit side-chains
   revert: symmetry clash
REVERT: A  728 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8926 (pp)
REVERT: A  749 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7614 (pp)
REVERT: A 1192 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8644 (mm)
REVERT: F  137 GLU cc_start: 0.7795 (tt0) cc_final: 0.7593 (tt0)
  outliers start: 48
  outliers final: 40
  residues processed: 152
  average time/residue: 0.3069
  time to fit residues: 78.1434
Evaluate side-chains
  160 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 117
  time to evaluate  : 2.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ASN
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  659 MET
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain A residue  870 MET
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  972 TYR
Chi-restraints excluded: chain A residue  990 ILE
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1168 MET
Chi-restraints excluded: chain A residue 1192 ILE
Chi-restraints excluded: chain A residue 1315 TYR
Chi-restraints excluded: chain A residue 1363 LEU
Chi-restraints excluded: chain A residue 1425 LEU
Chi-restraints excluded: chain A residue 1490 VAL
Chi-restraints excluded: chain A residue 1806 ILE
Chi-restraints excluded: chain A residue 1874 ASN
Chi-restraints excluded: chain A residue 2027 LEU
Chi-restraints excluded: chain A residue 2030 ASP
Chi-restraints excluded: chain A residue 2184 TYR
Chi-restraints excluded: chain A residue 2187 LEU
Chi-restraints excluded: chain A residue 2211 THR
Chi-restraints excluded: chain A residue 2259 LEU
Chi-restraints excluded: chain A residue 2277 MET
Chi-restraints excluded: chain B residue   27 TYR
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   76 ILE
Chi-restraints excluded: chain F residue  130 THR
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain F residue  331 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 236 optimal weight:   20.0000
   chunk 17 optimal weight:    4.9990
   chunk 142 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 194 optimal weight:    4.9990
   chunk 166 optimal weight:    0.0570
   chunk 131 optimal weight:    5.9990
   chunk 252 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    3.0106

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

Flipped N/Q/H residues before XYZ refinement:
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2001 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 = 0.3230 r_free = 0.3230 target = 0.073707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.061882 restraints weight = 56989.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.063237 restraints weight = 32441.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.064340 restraints weight = 23840.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  20984  Z= 0.176
  Angle     :  0.535   9.249  28466  Z= 0.278
  Chirality :  0.042   0.144   3094
  Planarity :  0.003   0.050   3766
  Dihedral  :  5.271  41.253   2842
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 46.36
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 18.60 %
    Favored  : 81.32 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.67 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.28 (0.16), residues: 2559
  helix: -2.03 (0.30), residues: 252
  sheet: -2.83 (0.17), residues: 886
  loop : -3.05 (0.16), residues: 1421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1996 
 HIS   0.003   0.001   HIS A1672 
 PHE   0.028   0.001   PHE A2257 
 TYR   0.014   0.001   TYR A1120 
 ARG   0.003   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02850 (  114)
  hydrogen bonds       : angle       4.93905 (  291)
  covalent geometry    : bond        0.00398 (20984)
  covalent geometry    : angle       0.53538 (28466)

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

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

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 118
  time to evaluate  : 2.382 
Fit side-chains
   revert: symmetry clash
REVERT: A  728 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8948 (pp)
REVERT: A  749 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7617 (pp)
REVERT: A 1192 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8692 (mm)
REVERT: B   54 TYR cc_start: 0.8455 (m-80) cc_final: 0.8130 (m-80)
REVERT: F  137 GLU cc_start: 0.7809 (tt0) cc_final: 0.7572 (tt0)
  outliers start: 48
  outliers final: 42
  residues processed: 152
  average time/residue: 0.3093
  time to fit residues: 77.7322
Evaluate side-chains
  162 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 117
  time to evaluate  : 2.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ASN
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  659 MET
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain A residue  870 MET
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  972 TYR
Chi-restraints excluded: chain A residue  990 ILE
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1168 MET
Chi-restraints excluded: chain A residue 1192 ILE
Chi-restraints excluded: chain A residue 1243 MET
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1315 TYR
Chi-restraints excluded: chain A residue 1363 LEU
Chi-restraints excluded: chain A residue 1425 LEU
Chi-restraints excluded: chain A residue 1490 VAL
Chi-restraints excluded: chain A residue 1806 ILE
Chi-restraints excluded: chain A residue 1857 THR
Chi-restraints excluded: chain A residue 1874 ASN
Chi-restraints excluded: chain A residue 2027 LEU
Chi-restraints excluded: chain A residue 2030 ASP
Chi-restraints excluded: chain A residue 2187 LEU
Chi-restraints excluded: chain A residue 2211 THR
Chi-restraints excluded: chain A residue 2259 LEU
Chi-restraints excluded: chain A residue 2277 MET
Chi-restraints excluded: chain A residue 2370 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   76 ILE
Chi-restraints excluded: chain F residue  130 THR
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain F residue  331 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 179 optimal weight:    1.9990
   chunk 92 optimal weight:    6.9990
   chunk 119 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 234 optimal weight:    9.9990
   chunk 65 optimal weight:   10.0000
   chunk 172 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   chunk 240 optimal weight:    9.9990
   chunk 125 optimal weight:   10.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1047 GLN
** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1395 GLN
** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2213 ASN
A2244 ASN
** A2344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 333 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.072839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.060903 restraints weight = 57290.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.062410 restraints weight = 32783.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.063372 restraints weight = 23881.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  20984  Z= 0.234
  Angle     :  0.583   9.688  28466  Z= 0.303
  Chirality :  0.044   0.155   3094
  Planarity :  0.004   0.049   3766
  Dihedral  :  5.460  34.599   2842
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 47.17
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  : 20.09 %
    Favored  : 79.87 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.54 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.33 (0.16), residues: 2559
  helix: -2.15 (0.29), residues: 258
  sheet: -2.82 (0.17), residues: 892
  loop : -3.10 (0.16), residues: 1409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A1996 
 HIS   0.004   0.001   HIS A1672 
 PHE   0.029   0.001   PHE A2257 
 TYR   0.017   0.002   TYR A1120 
 ARG   0.004   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03154 (  114)
  hydrogen bonds       : angle       5.12181 (  291)
  covalent geometry    : bond        0.00532 (20984)
  covalent geometry    : angle       0.58337 (28466)

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

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

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5118 Ramachandran restraints generated.
    2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 112
  time to evaluate  : 3.599 
Fit side-chains
   revert: symmetry clash
REVERT: A  728 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8960 (pp)
REVERT: A  749 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7611 (pp)
REVERT: A 1192 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8734 (mm)
REVERT: F  137 GLU cc_start: 0.7824 (tt0) cc_final: 0.7565 (tt0)
  outliers start: 49
  outliers final: 42
  residues processed: 148
  average time/residue: 0.3815
  time to fit residues: 94.7040
Evaluate side-chains
  156 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 111
  time to evaluate  : 3.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ASN
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  659 MET
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  758 MET
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain A residue  870 MET
Chi-restraints excluded: chain A residue  962 LEU
Chi-restraints excluded: chain A residue  972 TYR
Chi-restraints excluded: chain A residue  990 ILE
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1168 MET
Chi-restraints excluded: chain A residue 1192 ILE
Chi-restraints excluded: chain A residue 1243 MET
Chi-restraints excluded: chain A residue 1251 THR
Chi-restraints excluded: chain A residue 1315 TYR
Chi-restraints excluded: chain A residue 1363 LEU
Chi-restraints excluded: chain A residue 1425 LEU
Chi-restraints excluded: chain A residue 1490 VAL
Chi-restraints excluded: chain A residue 1806 ILE
Chi-restraints excluded: chain A residue 1857 THR
Chi-restraints excluded: chain A residue 1874 ASN
Chi-restraints excluded: chain A residue 2027 LEU
Chi-restraints excluded: chain A residue 2030 ASP
Chi-restraints excluded: chain A residue 2187 LEU
Chi-restraints excluded: chain A residue 2211 THR
Chi-restraints excluded: chain A residue 2259 LEU
Chi-restraints excluded: chain A residue 2277 MET
Chi-restraints excluded: chain A residue 2370 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   76 ILE
Chi-restraints excluded: chain F residue  130 THR
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain F residue  256 LEU
Chi-restraints excluded: chain F residue  331 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 78 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 132 optimal weight:    3.9990
   chunk 227 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1395 GLN
** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2213 ASN
A2244 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.072992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.061099 restraints weight = 57370.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.062555 restraints weight = 32724.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.063628 restraints weight = 23815.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  20984  Z= 0.213
  Angle     :  0.567   9.608  28466  Z= 0.294
  Chirality :  0.043   0.146   3094
  Planarity :  0.003   0.050   3766
  Dihedral  :  5.415  35.428   2842
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 46.93
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 19.50 %
    Favored  : 80.42 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.58 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.30 (0.16), residues: 2559
  helix: -2.06 (0.30), residues: 251
  sheet: -2.82 (0.17), residues: 896
  loop : -3.08 (0.16), residues: 1412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1996 
 HIS   0.004   0.001   HIS A1672 
 PHE   0.032   0.001   PHE A2257 
 TYR   0.017   0.001   TYR A1120 
 ARG   0.003   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03065 (  114)
  hydrogen bonds       : angle       5.05022 (  291)
  covalent geometry    : bond        0.00483 (20984)
  covalent geometry    : angle       0.56709 (28466)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5538.26 seconds
wall clock time: 99 minutes 43.61 seconds (5983.61 seconds total)