Starting phenix.real_space_refine
on Wed Feb  4 18:42:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wcb_65859/02_2026/9wcb_65859.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wcb_65859/02_2026/9wcb_65859.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wcb_65859/02_2026/9wcb_65859.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wcb_65859/02_2026/9wcb_65859.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wcb_65859/02_2026/9wcb_65859.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wcb_65859/02_2026/9wcb_65859.map"
  }
  resolution = 3.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.054
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    7545      2.51       5
     N    2076      2.21       5
     O    2472      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12120
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "J"
      Number of atoms: 1319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1319
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 5, 'TRANS': 168}
    Chain: "A"
      Number of atoms: 2721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2721
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 3, 'TRANS': 342}
    Chain: "F"
      Number of atoms: 1319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1319
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 5, 'TRANS': 168}
    Chain: "B"
      Number of atoms: 2721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2721
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 3, 'TRANS': 342}
    Chain: "Z"
      Number of atoms: 1319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1319
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 5, 'TRANS': 168}
    Chain: "C"
      Number of atoms: 2721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2721
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 3, 'TRANS': 342}
  Time building chain proxies: 2.70, per 1000 atoms: 0.22
  Number of scatterers: 12120
  At special positions: 0
  Unit cell: (90.72, 93.96, 138.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    2472      8.00
     N    2076      7.00
     C    7545      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 532.3 milliseconds
  

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2772

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 16 sheets defined
      6.6% alpha, 27.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'J' and resid 1104 through 1108
    Processing helix  chain 'A' and resid 95 through 102
      removed outlier: 3.681A  pdb=" N   VAL A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 139
    Processing helix  chain 'A' and resid 167 through 171
    Processing helix  chain 'A' and resid 199 through 204
      removed outlier: 3.663A  pdb=" N   SER A 204 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 330
    Processing helix  chain 'F' and resid 1104 through 1108
    Processing helix  chain 'B' and resid 95 through 102
      removed outlier: 3.562A  pdb=" N   VAL B 100 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 139
    Processing helix  chain 'B' and resid 167 through 171
    Processing helix  chain 'B' and resid 199 through 204
      removed outlier: 3.668A  pdb=" N   SER B 204 " --> pdb=" O   ASP B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 331
    Processing helix  chain 'Z' and resid 1104 through 1108
    Processing helix  chain 'C' and resid 95 through 102
      removed outlier: 3.677A  pdb=" N   VAL C 100 " --> pdb=" O   VAL C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 139
    Processing helix  chain 'C' and resid 199 through 203
    Processing helix  chain 'C' and resid 324 through 330
    Processing sheet with id=AA1, first strand: chain 'F' and resid 975 through 976
      removed outlier: 3.840A  pdb=" N   ASN F 975 " --> pdb=" O   ASN J 969 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   GLY Z 964 " --> pdb=" O   ASN J 969 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   GLY J 971 " --> pdb=" O   GLY Z 964 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 982 through 984
    Processing sheet with id=AA3, first strand: chain 'F' and resid 993 through 995
      removed outlier: 5.959A  pdb=" N   LEU J 988 " --> pdb=" O   GLU F 994 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'J' and resid 992 through 995
      removed outlier: 3.647A  pdb=" N   LEU Z 988 " --> pdb=" O   GLN J 992 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'J' and resid 999 through 1003
  WARNING: can't find start of bonding for strands!
    previous: chain 'J' and resid 999 through 1003
    current: chain 'J' and resid 1079 through 1083
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'J' and resid 1014 through 1020
  WARNING: can't find start of bonding for strands!
    previous: chain 'J' and resid 1014 through 1020
    current: chain 'J' and resid 1053 through 1064
      removed outlier: 6.811A  pdb=" N   VAL J1062 " --> pdb=" O   ILE J1069 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 12 through 24
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 31 through 32
    current: chain 'A' and resid 50 through 54
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 50 through 54
    current: chain 'A' and resid 86 through 91
      removed outlier: 4.297A  pdb=" N   LEU A 271 " --> pdb=" O   ALA A 259 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 267 through 273
    current: chain 'A' and resid 310 through 319
    Processing sheet with id=AA8, first strand: chain 'A' and resid 242 through 243
      removed outlier: 3.889A  pdb=" N   GLY A 247 " --> pdb=" O   VAL A 243 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 999 through 1003
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 999 through 1003
    current: chain 'F' and resid 1079 through 1083
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'F' and resid 1014 through 1020
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 1014 through 1020
    current: chain 'F' and resid 1053 through 1064
      removed outlier: 6.820A  pdb=" N   VAL F1062 " --> pdb=" O   ILE F1069 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 12 through 24
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 31 through 32
    current: chain 'B' and resid 51 through 54
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 51 through 54
    current: chain 'B' and resid 86 through 91
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 267 through 273
    current: chain 'B' and resid 310 through 319
    Processing sheet with id=AB3, first strand: chain 'B' and resid 242 through 243
      removed outlier: 3.836A  pdb=" N   GLY B 247 " --> pdb=" O   VAL B 243 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'Z' and resid 999 through 1003
  WARNING: can't find start of bonding for strands!
    previous: chain 'Z' and resid 999 through 1003
    current: chain 'Z' and resid 1079 through 1083
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'Z' and resid 1014 through 1020
  WARNING: can't find start of bonding for strands!
    previous: chain 'Z' and resid 1014 through 1020
    current: chain 'Z' and resid 1053 through 1064
      removed outlier: 6.829A  pdb=" N   VAL Z1062 " --> pdb=" O   ILE Z1069 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 12 through 24
      removed outlier: 3.531A  pdb=" N   GLY C  31 " --> pdb=" O   TYR C  22 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 31 through 32
    current: chain 'C' and resid 50 through 54
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 50 through 54
    current: chain 'C' and resid 86 through 91
      removed outlier: 4.225A  pdb=" N   LEU C 271 " --> pdb=" O   ALA C 259 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 267 through 273
    current: chain 'C' and resid 310 through 319
    Processing sheet with id=AB7, first strand: chain 'C' and resid 242 through 243
      removed outlier: 3.697A  pdb=" N   GLY C 247 " --> pdb=" O   VAL C 243 " (cutoff:3.500A)

    287 hydrogen bonds defined for protein.
    723 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.85

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4111
        1.34 -     1.46: 2773
        1.46 -     1.57: 5419
        1.57 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 12351
  Sorted by residual:
  bond pdb=" CG  MET C  36 "
       pdb=" SD  MET C  36 "
    ideal  model  delta    sigma   weight residual
    1.803  1.772  0.031 2.50e-02 1.60e+03 1.53e+00
  bond pdb=" CB  VAL F1062 "
       pdb=" CG1 VAL F1062 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.33e+00
  bond pdb=" CB  ASP A  18 "
       pdb=" CG  ASP A  18 "
    ideal  model  delta    sigma   weight residual
    1.516  1.488  0.028 2.50e-02 1.60e+03 1.28e+00
  bond pdb=" CG  MET B  36 "
       pdb=" SD  MET B  36 "
    ideal  model  delta    sigma   weight residual
    1.803  1.775  0.028 2.50e-02 1.60e+03 1.24e+00
  bond pdb=" CB  VAL J1062 "
       pdb=" CG1 VAL J1062 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.04e+00
  ... (remaining 12346 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 16299
        1.64 -     3.28: 370
        3.28 -     4.93: 50
        4.93 -     6.57: 10
        6.57 -     8.21: 2
  Bond angle restraints: 16731
  Sorted by residual:
  angle pdb=" N   LYS B 308 "
        pdb=" CA  LYS B 308 "
        pdb=" C   LYS B 308 "
      ideal   model   delta    sigma   weight residual
     114.75  109.95    4.80 1.26e+00 6.30e-01 1.45e+01
  angle pdb=" CA  GLU C 185 "
        pdb=" CB  GLU C 185 "
        pdb=" CG  GLU C 185 "
      ideal   model   delta    sigma   weight residual
     114.10  119.96   -5.86 2.00e+00 2.50e-01 8.58e+00
  angle pdb=" CA  GLN J 992 "
        pdb=" CB  GLN J 992 "
        pdb=" CG  GLN J 992 "
      ideal   model   delta    sigma   weight residual
     114.10  119.51   -5.41 2.00e+00 2.50e-01 7.32e+00
  angle pdb=" CA  ILE J1069 "
        pdb=" C   ILE J1069 "
        pdb=" N   PHE J1070 "
      ideal   model   delta    sigma   weight residual
     116.60  120.48   -3.88 1.45e+00 4.76e-01 7.17e+00
  angle pdb=" N   GLY C  19 "
        pdb=" CA  GLY C  19 "
        pdb=" C   GLY C  19 "
      ideal   model   delta    sigma   weight residual
     113.18  107.01    6.17 2.37e+00 1.78e-01 6.77e+00
  ... (remaining 16726 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 6175
       17.87 -    35.74: 738
       35.74 -    53.61: 180
       53.61 -    71.48: 50
       71.48 -    89.35: 15
  Dihedral angle restraints: 7158
    sinusoidal: 2736
      harmonic: 4422
  Sorted by residual:
  dihedral pdb=" CA  TYR C 184 "
           pdb=" C   TYR C 184 "
           pdb=" N   GLU C 185 "
           pdb=" CA  GLU C 185 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.06  -22.94     0      5.00e+00 4.00e-02 2.11e+01
  dihedral pdb=" CA  MET F1122 "
           pdb=" C   MET F1122 "
           pdb=" N   LYS F1123 "
           pdb=" CA  LYS F1123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.54   18.46     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  GLY C  19 "
           pdb=" C   GLY C  19 "
           pdb=" N   LEU C  20 "
           pdb=" CA  LEU C  20 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.82  -18.18     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 7155 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1147
       0.036 -    0.073: 448
       0.073 -    0.109: 116
       0.109 -    0.146: 66
       0.146 -    0.182: 2
  Chirality restraints: 1779
  Sorted by residual:
  chirality pdb=" CB  VAL A 343 "
            pdb=" CA  VAL A 343 "
            pdb=" CG1 VAL A 343 "
            pdb=" CG2 VAL A 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.30e-01
  chirality pdb=" CB  VAL Z 966 "
            pdb=" CA  VAL Z 966 "
            pdb=" CG1 VAL Z 966 "
            pdb=" CG2 VAL Z 966 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.21e-01
  chirality pdb=" CA  ILE A 189 "
            pdb=" N   ILE A 189 "
            pdb=" C   ILE A 189 "
            pdb=" CB  ILE A 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.13e-01
  ... (remaining 1776 not shown)

  Planarity restraints: 2238
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE J1032 "   -0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO J1033 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO J1033 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO J1033 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 185 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.68e+00
        pdb=" CD  GLU C 185 "    0.028 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 185 "   -0.010 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 185 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 268 "    0.025 5.00e-02 4.00e+02   3.90e-02 2.43e+00
        pdb=" N   PRO A 269 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 269 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 269 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2235 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 689
        2.72 -     3.26: 12376
        3.26 -     3.81: 19352
        3.81 -     4.35: 24327
        4.35 -     4.90: 42538
  Nonbonded interactions: 99282
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B  89 "
            pdb=" OG1 THR B 130 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" OE1 GLN Z1024 "
            pdb=" N   LYS Z1025 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" NH1 ARG B  92 "
            pdb=" O   GLY B 125 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OD2 ASP A  99 "
            pdb=" NH1 ARG A 132 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" OH  TYR C  22 "
            pdb=" OE2 GLU C 109 "
     model   vdw
     2.223 3.040
  ... (remaining 99277 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'J'
  selection = chain 'Z'
}

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:             2.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.830
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
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      :  0.004   0.038  12351  Z= 0.165
  Angle     :  0.608   8.211  16731  Z= 0.343
  Chirality :  0.045   0.182   1779
  Planarity :  0.003   0.041   2238
  Dihedral  : 17.003  89.352   4386
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 29.01 %
    Favored  : 70.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.22), residues: 1548
  helix: -3.50 (0.41), residues: 45
  sheet: -0.02 (0.19), residues: 810
  loop : -1.87 (0.23), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Z1019 
 TYR   0.016   0.001   TYR C 149 
 PHE   0.015   0.002   PHE A 187 
 TRP   0.023   0.001   TRP C 248 
 HIS   0.002   0.001   HIS F1042 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (12351)
  covalent geometry    : angle       0.60822 (16731)
  hydrogen bonds       : bond        0.15063 (  287)
  hydrogen bonds       : angle       6.11546 (  723)

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

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

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 233
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  987 LYS cc_start: 0.8304 (tttm) cc_final: 0.8039 (tttt)
REVERT: J  994 GLU cc_start: 0.7534 (tt0) cc_final: 0.7247 (tt0)
REVERT: A  276 SER cc_start: 0.9078 (t) cc_final: 0.8741 (p)
REVERT: F 1025 LYS cc_start: 0.9011 (mttt) cc_final: 0.8794 (mtmm)
REVERT: F 1067 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7328 (mp10)
REVERT: B  131 TYR cc_start: 0.8663 (t80) cc_final: 0.8195 (t80)
REVERT: Z  994 GLU cc_start: 0.7692 (tt0) cc_final: 0.7457 (tt0)
  outliers start: 4
  outliers final: 1
  residues processed: 235
  average time/residue: 0.1293
  time to fit residues: 41.9167
Evaluate side-chains
  208 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 123 GLN
A 126 ASN
A 150 GLN
A 153 ASN
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 ASN
** F 974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1048 ASN
F1106 ASN
B   9 ASN
** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 150 GLN
B 153 ASN
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 172 ASN
C  21 HIS
C 126 ASN
C 153 ASN
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
C 250 ASN
C 254 ASN
C 309 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.116248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.095690 restraints weight = 16920.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.098842 restraints weight = 9667.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.100955 restraints weight = 6580.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.102442 restraints weight = 5000.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.103426 restraints weight = 4089.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.1125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12351  Z= 0.174
  Angle     :  0.571   5.873  16731  Z= 0.316
  Chirality :  0.044   0.203   1779
  Planarity :  0.003   0.039   2238
  Dihedral  :  4.632  20.958   1711
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 25.46 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.22), residues: 1548
  helix: -3.10 (0.49), residues: 45
  sheet:  0.00 (0.20), residues: 813
  loop : -1.93 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG Z1019 
 TYR   0.017   0.001   TYR C 149 
 PHE   0.017   0.001   PHE Z1070 
 TRP   0.016   0.001   TRP C 248 
 HIS   0.004   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (12351)
  covalent geometry    : angle       0.57092 (16731)
  hydrogen bonds       : bond        0.02920 (  287)
  hydrogen bonds       : angle       5.34069 (  723)

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

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

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 227
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  992 GLN cc_start: 0.8481 (pm20) cc_final: 0.8161 (pm20)
REVERT: J 1067 GLN cc_start: 0.7631 (mp10) cc_final: 0.7202 (mp10)
REVERT: A  148 GLN cc_start: 0.8703 (tt0) cc_final: 0.8348 (mt0)
REVERT: A  164 ASN cc_start: 0.8937 (p0) cc_final: 0.8539 (p0)
REVERT: A  308 LYS cc_start: 0.8430 (tptp) cc_final: 0.8226 (tptt)
REVERT: A  328 ARG cc_start: 0.9053 (ptp-110) cc_final: 0.8821 (ptp-110)
REVERT: F  989 SER cc_start: 0.8584 (t) cc_final: 0.7849 (p)
REVERT: F 1048 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7765 (p0)
REVERT: B  131 TYR cc_start: 0.8717 (t80) cc_final: 0.8325 (t80)
REVERT: B  144 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8039 (m-40)
REVERT: Z  992 GLN cc_start: 0.8887 (pm20) cc_final: 0.8661 (pm20)
REVERT: Z  994 GLU cc_start: 0.7473 (tt0) cc_final: 0.7200 (tt0)
REVERT: C   49 GLN cc_start: 0.7513 (mp10) cc_final: 0.7111 (pm20)
  outliers start: 56
  outliers final: 24
  residues processed: 264
  average time/residue: 0.1110
  time to fit residues: 41.4008
Evaluate side-chains
  229 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 203
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  998 VAL
Chi-restraints excluded: chain J residue 1068 GLU
Chi-restraints excluded: chain J residue 1126 THR
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain F residue  982 CYS
Chi-restraints excluded: chain F residue  997 ILE
Chi-restraints excluded: chain F residue 1048 ASN
Chi-restraints excluded: chain F residue 1068 GLU
Chi-restraints excluded: chain F residue 1115 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain Z residue  976 VAL
Chi-restraints excluded: chain Z residue 1000 THR
Chi-restraints excluded: chain Z residue 1062 VAL
Chi-restraints excluded: chain Z residue 1113 SER
Chi-restraints excluded: chain Z residue 1119 VAL
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  126 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 137 optimal weight:    4.9990
   chunk 83 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
J1106 ASN
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  70 ASN
A 123 GLN
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1048 ASN
** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 150 GLN
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 250 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.115160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.094624 restraints weight = 17166.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.097742 restraints weight = 9794.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.099874 restraints weight = 6648.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.101280 restraints weight = 5060.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.102260 restraints weight = 4136.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12351  Z= 0.190
  Angle     :  0.570   6.762  16731  Z= 0.315
  Chirality :  0.044   0.201   1779
  Planarity :  0.003   0.037   2238
  Dihedral  :  4.632  18.507   1710
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 25.77 %
    Favored  : 69.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.22), residues: 1548
  helix: -3.03 (0.52), residues: 45
  sheet: -0.05 (0.20), residues: 813
  loop : -1.99 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Z1019 
 TYR   0.012   0.001   TYR B 297 
 PHE   0.016   0.002   PHE Z1070 
 TRP   0.015   0.001   TRP C  56 
 HIS   0.005   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (12351)
  covalent geometry    : angle       0.56977 (16731)
  hydrogen bonds       : bond        0.02789 (  287)
  hydrogen bonds       : angle       5.37328 (  723)

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

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

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 215
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: J  992 GLN cc_start: 0.8542 (pm20) cc_final: 0.8047 (pm20)
REVERT: J 1038 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8216 (ttm-80)
REVERT: J 1067 GLN cc_start: 0.7592 (mp10) cc_final: 0.7108 (mp10)
REVERT: A   41 LYS cc_start: 0.8322 (mtmm) cc_final: 0.8024 (ttpt)
REVERT: A  164 ASN cc_start: 0.8897 (p0) cc_final: 0.8452 (p0)
REVERT: F  989 SER cc_start: 0.8604 (t) cc_final: 0.7871 (p)
REVERT: F 1048 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7633 (p0)
REVERT: F 1067 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7536 (mp10)
REVERT: F 1087 MET cc_start: 0.8333 (ptm) cc_final: 0.8021 (ptm)
REVERT: B  131 TYR cc_start: 0.8713 (t80) cc_final: 0.8329 (t80)
REVERT: B  144 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8059 (m-40)
REVERT: Z  983 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7263 (tm-30)
REVERT: Z  992 GLN cc_start: 0.8916 (pm20) cc_final: 0.8511 (pm20)
REVERT: Z  994 GLU cc_start: 0.7438 (tt0) cc_final: 0.7170 (tt0)
REVERT: Z 1026 PHE cc_start: 0.8776 (p90) cc_final: 0.8330 (p90)
REVERT: Z 1067 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7306 (mp10)
REVERT: C  149 TYR cc_start: 0.7865 (t80) cc_final: 0.7466 (t80)
  outliers start: 55
  outliers final: 38
  residues processed: 254
  average time/residue: 0.1204
  time to fit residues: 42.9064
Evaluate side-chains
  248 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 206
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue 1038 ARG
Chi-restraints excluded: chain J residue 1062 VAL
Chi-restraints excluded: chain J residue 1068 GLU
Chi-restraints excluded: chain J residue 1126 THR
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain F residue  982 CYS
Chi-restraints excluded: chain F residue  997 ILE
Chi-restraints excluded: chain F residue  998 VAL
Chi-restraints excluded: chain F residue 1048 ASN
Chi-restraints excluded: chain F residue 1062 VAL
Chi-restraints excluded: chain F residue 1068 GLU
Chi-restraints excluded: chain F residue 1113 SER
Chi-restraints excluded: chain F residue 1115 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  204 SER
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain Z residue  983 GLN
Chi-restraints excluded: chain Z residue 1000 THR
Chi-restraints excluded: chain Z residue 1060 LEU
Chi-restraints excluded: chain Z residue 1062 VAL
Chi-restraints excluded: chain Z residue 1068 GLU
Chi-restraints excluded: chain Z residue 1113 SER
Chi-restraints excluded: chain Z residue 1117 LEU
Chi-restraints excluded: chain Z residue 1119 VAL
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  141 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 147 optimal weight:    0.4980
   chunk 113 optimal weight:    0.1980
   chunk 33 optimal weight:    1.9990
   chunk 138 optimal weight:    5.9990
   chunk 135 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
J1106 ASN
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 123 GLN
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1048 ASN
F1106 ASN
** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z1106 ASN
** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 250 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.117509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.097082 restraints weight = 16919.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.100196 restraints weight = 9669.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.102310 restraints weight = 6588.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.103722 restraints weight = 5007.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.104721 restraints weight = 4097.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  12351  Z= 0.162
  Angle     :  0.555   8.593  16731  Z= 0.305
  Chirality :  0.044   0.212   1779
  Planarity :  0.003   0.032   2238
  Dihedral  :  4.573  19.165   1710
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 25.69 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.22), residues: 1548
  helix: -2.87 (0.54), residues: 45
  sheet: -0.07 (0.20), residues: 816
  loop : -1.97 (0.23), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F1061 
 TYR   0.015   0.001   TYR A 184 
 PHE   0.015   0.002   PHE B 136 
 TRP   0.011   0.001   TRP C 248 
 HIS   0.005   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (12351)
  covalent geometry    : angle       0.55463 (16731)
  hydrogen bonds       : bond        0.02557 (  287)
  hydrogen bonds       : angle       5.31777 (  723)

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

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

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 220
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
REVERT: J  992 GLN cc_start: 0.8596 (pm20) cc_final: 0.8033 (pm20)
REVERT: J 1038 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8200 (ttm-80)
REVERT: J 1067 GLN cc_start: 0.7594 (mp10) cc_final: 0.7135 (mp10)
REVERT: A  164 ASN cc_start: 0.8911 (p0) cc_final: 0.8443 (p0)
REVERT: F  989 SER cc_start: 0.8629 (t) cc_final: 0.8007 (p)
REVERT: F 1048 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7609 (p0)
REVERT: B  131 TYR cc_start: 0.8777 (t80) cc_final: 0.8410 (t80)
REVERT: B  308 LYS cc_start: 0.8563 (tmtt) cc_final: 0.7915 (tptp)
REVERT: Z  983 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7231 (tm-30)
REVERT: Z  992 GLN cc_start: 0.8923 (pm20) cc_final: 0.8468 (pm20)
REVERT: Z  994 GLU cc_start: 0.7504 (tt0) cc_final: 0.7246 (tt0)
REVERT: Z 1026 PHE cc_start: 0.8760 (p90) cc_final: 0.8260 (p90)
REVERT: Z 1067 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7269 (mp10)
REVERT: C   21 HIS cc_start: 0.8844 (OUTLIER) cc_final: 0.8479 (t70)
REVERT: C   32 ASP cc_start: 0.8601 (t70) cc_final: 0.8388 (t70)
REVERT: C  149 TYR cc_start: 0.7937 (t80) cc_final: 0.7533 (t80)
  outliers start: 60
  outliers final: 41
  residues processed: 265
  average time/residue: 0.1133
  time to fit residues: 42.8801
Evaluate side-chains
  248 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 203
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue 1038 ARG
Chi-restraints excluded: chain J residue 1062 VAL
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain F residue  982 CYS
Chi-restraints excluded: chain F residue  998 VAL
Chi-restraints excluded: chain F residue 1048 ASN
Chi-restraints excluded: chain F residue 1062 VAL
Chi-restraints excluded: chain F residue 1068 GLU
Chi-restraints excluded: chain F residue 1113 SER
Chi-restraints excluded: chain F residue 1115 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain Z residue  972 THR
Chi-restraints excluded: chain Z residue  983 GLN
Chi-restraints excluded: chain Z residue  984 ILE
Chi-restraints excluded: chain Z residue  998 VAL
Chi-restraints excluded: chain Z residue 1000 THR
Chi-restraints excluded: chain Z residue 1060 LEU
Chi-restraints excluded: chain Z residue 1062 VAL
Chi-restraints excluded: chain Z residue 1068 GLU
Chi-restraints excluded: chain Z residue 1099 THR
Chi-restraints excluded: chain Z residue 1113 SER
Chi-restraints excluded: chain Z residue 1117 LEU
Chi-restraints excluded: chain Z residue 1119 VAL
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  345 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 132 optimal weight:    4.9990
   chunk 122 optimal weight:    0.7980
   chunk 149 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 139 optimal weight:    0.0770
   chunk 69 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 114 optimal weight:    2.9990
   chunk 147 optimal weight:    0.9990
   overall best weight:    0.9342

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 123 GLN
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1048 ASN
** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z1106 ASN
** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 250 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.116125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.095615 restraints weight = 17052.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.098710 restraints weight = 9737.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.100808 restraints weight = 6616.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.102262 restraints weight = 5044.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.103242 restraints weight = 4116.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  12351  Z= 0.161
  Angle     :  0.556   7.642  16731  Z= 0.304
  Chirality :  0.043   0.218   1779
  Planarity :  0.003   0.030   2238
  Dihedral  :  4.528  17.369   1710
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 26.16 %
    Favored  : 69.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.22), residues: 1548
  helix: -2.74 (0.58), residues: 45
  sheet: -0.09 (0.20), residues: 819
  loop : -1.99 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J1019 
 TYR   0.013   0.001   TYR A 184 
 PHE   0.018   0.001   PHE Z1070 
 TRP   0.018   0.001   TRP C  56 
 HIS   0.005   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (12351)
  covalent geometry    : angle       0.55572 (16731)
  hydrogen bonds       : bond        0.02555 (  287)
  hydrogen bonds       : angle       5.28982 (  723)

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

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

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 223
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: J  992 GLN cc_start: 0.8617 (pm20) cc_final: 0.8014 (pm20)
REVERT: J 1038 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8195 (ttm-80)
REVERT: J 1067 GLN cc_start: 0.7624 (mp10) cc_final: 0.7168 (mp10)
REVERT: A  164 ASN cc_start: 0.8901 (p0) cc_final: 0.8454 (p0)
REVERT: A  308 LYS cc_start: 0.8313 (tptt) cc_final: 0.8096 (tptp)
REVERT: F  989 SER cc_start: 0.8657 (t) cc_final: 0.8018 (p)
REVERT: F 1048 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7729 (p0)
REVERT: B  131 TYR cc_start: 0.8783 (t80) cc_final: 0.8409 (t80)
REVERT: B  144 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8030 (m-40)
REVERT: B  238 TYR cc_start: 0.8051 (m-10) cc_final: 0.7769 (m-10)
REVERT: B  308 LYS cc_start: 0.8525 (tmtt) cc_final: 0.7997 (tptp)
REVERT: Z  983 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7235 (tm-30)
REVERT: Z  992 GLN cc_start: 0.8949 (pm20) cc_final: 0.8409 (pm20)
REVERT: Z  994 GLU cc_start: 0.7502 (tt0) cc_final: 0.7236 (tt0)
REVERT: Z 1022 ASP cc_start: 0.8774 (t0) cc_final: 0.8528 (t0)
REVERT: Z 1067 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7441 (mp10)
REVERT: C   21 HIS cc_start: 0.8813 (OUTLIER) cc_final: 0.8450 (t70)
REVERT: C   32 ASP cc_start: 0.8583 (t70) cc_final: 0.8337 (t70)
REVERT: C  149 TYR cc_start: 0.7908 (t80) cc_final: 0.7574 (t80)
  outliers start: 57
  outliers final: 47
  residues processed: 265
  average time/residue: 0.1184
  time to fit residues: 44.4409
Evaluate side-chains
  263 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 211
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  981 ASN
Chi-restraints excluded: chain J residue 1038 ARG
Chi-restraints excluded: chain J residue 1062 VAL
Chi-restraints excluded: chain J residue 1068 GLU
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain F residue  982 CYS
Chi-restraints excluded: chain F residue 1047 SER
Chi-restraints excluded: chain F residue 1048 ASN
Chi-restraints excluded: chain F residue 1062 VAL
Chi-restraints excluded: chain F residue 1068 GLU
Chi-restraints excluded: chain F residue 1113 SER
Chi-restraints excluded: chain F residue 1115 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain Z residue  972 THR
Chi-restraints excluded: chain Z residue  983 GLN
Chi-restraints excluded: chain Z residue  984 ILE
Chi-restraints excluded: chain Z residue  998 VAL
Chi-restraints excluded: chain Z residue 1000 THR
Chi-restraints excluded: chain Z residue 1060 LEU
Chi-restraints excluded: chain Z residue 1062 VAL
Chi-restraints excluded: chain Z residue 1068 GLU
Chi-restraints excluded: chain Z residue 1099 THR
Chi-restraints excluded: chain Z residue 1113 SER
Chi-restraints excluded: chain Z residue 1117 LEU
Chi-restraints excluded: chain Z residue 1119 VAL
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  141 ASP
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  283 VAL
Chi-restraints excluded: chain C residue  345 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 151 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0670
   chunk 139 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 140 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 127 optimal weight:    3.9990
   chunk 122 optimal weight:    0.6980
   overall best weight:    0.9320

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 123 GLN
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1048 ASN
F1106 ASN
** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 163 ASN
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z1106 ASN
** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
C 250 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.116226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.095766 restraints weight = 17170.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.098888 restraints weight = 9779.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.101003 restraints weight = 6642.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.102418 restraints weight = 5054.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.103408 restraints weight = 4132.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  12351  Z= 0.161
  Angle     :  0.564   7.282  16731  Z= 0.308
  Chirality :  0.043   0.234   1779
  Planarity :  0.003   0.030   2238
  Dihedral  :  4.516  17.163   1710
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 26.00 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.22), residues: 1548
  helix: -2.66 (0.60), residues: 45
  sheet: -0.12 (0.20), residues: 819
  loop : -1.98 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J1019 
 TYR   0.013   0.001   TYR J1053 
 PHE   0.016   0.001   PHE Z1070 
 TRP   0.020   0.001   TRP C  56 
 HIS   0.004   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (12351)
  covalent geometry    : angle       0.56352 (16731)
  hydrogen bonds       : bond        0.02492 (  287)
  hydrogen bonds       : angle       5.27439 (  723)

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

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

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 222
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
REVERT: J  992 GLN cc_start: 0.8657 (pm20) cc_final: 0.8010 (pm20)
REVERT: J 1038 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8187 (ttm-80)
REVERT: J 1051 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.7820 (tm-30)
REVERT: J 1067 GLN cc_start: 0.7642 (mp10) cc_final: 0.7214 (mp10)
REVERT: A   41 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7883 (ttpt)
REVERT: A  308 LYS cc_start: 0.8375 (tptt) cc_final: 0.8139 (tptp)
REVERT: F  989 SER cc_start: 0.8692 (t) cc_final: 0.8052 (p)
REVERT: F 1087 MET cc_start: 0.8519 (ptm) cc_final: 0.8018 (ptm)
REVERT: B  131 TYR cc_start: 0.8773 (t80) cc_final: 0.8396 (t80)
REVERT: B  144 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8018 (m-40)
REVERT: B  155 SER cc_start: 0.9229 (p) cc_final: 0.8983 (t)
REVERT: B  238 TYR cc_start: 0.8074 (m-10) cc_final: 0.7783 (m-10)
REVERT: B  308 LYS cc_start: 0.8512 (tmtt) cc_final: 0.7996 (tptp)
REVERT: Z  983 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7229 (tm-30)
REVERT: Z  992 GLN cc_start: 0.8913 (pm20) cc_final: 0.8354 (pm20)
REVERT: Z  994 GLU cc_start: 0.7489 (tt0) cc_final: 0.7215 (tt0)
REVERT: Z 1022 ASP cc_start: 0.8772 (t0) cc_final: 0.8545 (t0)
REVERT: Z 1067 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7542 (mp10)
REVERT: C   21 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.8446 (t70)
REVERT: C   32 ASP cc_start: 0.8521 (t70) cc_final: 0.8306 (t70)
REVERT: C  149 TYR cc_start: 0.7922 (t80) cc_final: 0.7694 (t80)
  outliers start: 68
  outliers final: 52
  residues processed: 273
  average time/residue: 0.1091
  time to fit residues: 42.3504
Evaluate side-chains
  262 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 205
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  981 ASN
Chi-restraints excluded: chain J residue 1038 ARG
Chi-restraints excluded: chain J residue 1051 GLN
Chi-restraints excluded: chain J residue 1062 VAL
Chi-restraints excluded: chain J residue 1068 GLU
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain F residue  982 CYS
Chi-restraints excluded: chain F residue  998 VAL
Chi-restraints excluded: chain F residue 1062 VAL
Chi-restraints excluded: chain F residue 1068 GLU
Chi-restraints excluded: chain F residue 1113 SER
Chi-restraints excluded: chain F residue 1115 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  161 MET
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain Z residue  972 THR
Chi-restraints excluded: chain Z residue  983 GLN
Chi-restraints excluded: chain Z residue  984 ILE
Chi-restraints excluded: chain Z residue  998 VAL
Chi-restraints excluded: chain Z residue 1000 THR
Chi-restraints excluded: chain Z residue 1060 LEU
Chi-restraints excluded: chain Z residue 1062 VAL
Chi-restraints excluded: chain Z residue 1099 THR
Chi-restraints excluded: chain Z residue 1113 SER
Chi-restraints excluded: chain Z residue 1117 LEU
Chi-restraints excluded: chain Z residue 1119 VAL
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  141 ASP
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  172 ASN
Chi-restraints excluded: chain C residue  283 VAL
Chi-restraints excluded: chain C residue  345 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 131 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 146 optimal weight:    0.6980
   chunk 84 optimal weight:    6.9990
   chunk 96 optimal weight:    1.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
J1106 ASN
A 123 GLN
A 144 ASN
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1106 ASN
** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 163 ASN
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z1106 ASN
** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 150 GLN
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.111815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.090933 restraints weight = 17263.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.093983 restraints weight = 9990.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.096052 restraints weight = 6854.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.097460 restraints weight = 5281.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.098470 restraints weight = 4354.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12351  Z= 0.238
  Angle     :  0.616   8.595  16731  Z= 0.335
  Chirality :  0.045   0.249   1779
  Planarity :  0.003   0.031   2238
  Dihedral  :  4.706  17.276   1710
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.66 %
    Favored  : 89.34 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 26.16 %
    Favored  : 68.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.22), residues: 1548
  helix: -2.96 (0.54), residues: 45
  sheet: -0.17 (0.20), residues: 798
  loop : -2.05 (0.22), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J1019 
 TYR   0.016   0.001   TYR B 297 
 PHE   0.015   0.002   PHE B 136 
 TRP   0.016   0.001   TRP C  56 
 HIS   0.005   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 (12351)
  covalent geometry    : angle       0.61608 (16731)
  hydrogen bonds       : bond        0.02780 (  287)
  hydrogen bonds       : angle       5.38617 (  723)

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

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

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 219
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
REVERT: J  992 GLN cc_start: 0.8656 (pm20) cc_final: 0.8013 (pm20)
REVERT: J 1038 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8231 (ttm-80)
REVERT: J 1051 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.7828 (tm-30)
REVERT: J 1067 GLN cc_start: 0.7704 (mp10) cc_final: 0.7361 (mp10)
REVERT: A   41 LYS cc_start: 0.8351 (mtmm) cc_final: 0.7930 (ttpt)
REVERT: A  131 TYR cc_start: 0.8838 (t80) cc_final: 0.8491 (t80)
REVERT: F  989 SER cc_start: 0.8670 (t) cc_final: 0.7992 (p)
REVERT: F 1067 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7581 (mp10)
REVERT: F 1087 MET cc_start: 0.8466 (ptm) cc_final: 0.8198 (ptm)
REVERT: B  131 TYR cc_start: 0.8791 (t80) cc_final: 0.8414 (t80)
REVERT: B  144 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8083 (m-40)
REVERT: B  238 TYR cc_start: 0.8097 (m-10) cc_final: 0.7845 (m-10)
REVERT: Z  983 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7242 (tm-30)
REVERT: Z  992 GLN cc_start: 0.8874 (pm20) cc_final: 0.8333 (pm20)
REVERT: Z  994 GLU cc_start: 0.7535 (tt0) cc_final: 0.7294 (tt0)
REVERT: Z 1067 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7553 (mp10)
REVERT: C   21 HIS cc_start: 0.8787 (OUTLIER) cc_final: 0.8359 (t70)
REVERT: C   56 TRP cc_start: 0.9015 (t60) cc_final: 0.8797 (t60)
  outliers start: 65
  outliers final: 54
  residues processed: 265
  average time/residue: 0.1073
  time to fit residues: 40.1252
Evaluate side-chains
  263 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 204
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  981 ASN
Chi-restraints excluded: chain J residue  998 VAL
Chi-restraints excluded: chain J residue 1038 ARG
Chi-restraints excluded: chain J residue 1051 GLN
Chi-restraints excluded: chain J residue 1062 VAL
Chi-restraints excluded: chain J residue 1068 GLU
Chi-restraints excluded: chain J residue 1126 THR
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain F residue  982 CYS
Chi-restraints excluded: chain F residue  998 VAL
Chi-restraints excluded: chain F residue 1047 SER
Chi-restraints excluded: chain F residue 1062 VAL
Chi-restraints excluded: chain F residue 1068 GLU
Chi-restraints excluded: chain F residue 1100 VAL
Chi-restraints excluded: chain F residue 1113 SER
Chi-restraints excluded: chain F residue 1115 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain Z residue  972 THR
Chi-restraints excluded: chain Z residue  983 GLN
Chi-restraints excluded: chain Z residue  984 ILE
Chi-restraints excluded: chain Z residue  998 VAL
Chi-restraints excluded: chain Z residue 1000 THR
Chi-restraints excluded: chain Z residue 1060 LEU
Chi-restraints excluded: chain Z residue 1062 VAL
Chi-restraints excluded: chain Z residue 1068 GLU
Chi-restraints excluded: chain Z residue 1113 SER
Chi-restraints excluded: chain Z residue 1117 LEU
Chi-restraints excluded: chain Z residue 1119 VAL
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  141 ASP
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  172 ASN
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  283 VAL
Chi-restraints excluded: chain C residue  345 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 134 optimal weight:    0.0970
   chunk 11 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 139 optimal weight:    2.9990
   chunk 125 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 131 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
J1106 ASN
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 123 GLN
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1106 ASN
B 163 ASN
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z1106 ASN
C 148 GLN
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.121678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.101386 restraints weight = 16718.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.104532 restraints weight = 9489.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.106646 restraints weight = 6445.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.108076 restraints weight = 4898.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.109079 restraints weight = 3990.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12351  Z= 0.143
  Angle     :  0.582   8.437  16731  Z= 0.318
  Chirality :  0.044   0.263   1779
  Planarity :  0.003   0.029   2238
  Dihedral  :  4.564  17.704   1710
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 27.08 %
    Favored  : 68.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.22), residues: 1548
  helix: -2.58 (0.62), residues: 45
  sheet: -0.24 (0.20), residues: 816
  loop : -2.03 (0.23), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J1019 
 TYR   0.017   0.001   TYR C 149 
 PHE   0.025   0.001   PHE F1026 
 TRP   0.015   0.001   TRP C 248 
 HIS   0.005   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (12351)
  covalent geometry    : angle       0.58169 (16731)
  hydrogen bonds       : bond        0.02398 (  287)
  hydrogen bonds       : angle       5.23405 (  723)

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

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

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 225
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  992 GLN cc_start: 0.8616 (pm20) cc_final: 0.7973 (pm20)
REVERT: J 1038 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8188 (ttm-80)
REVERT: J 1051 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7761 (tm-30)
REVERT: J 1067 GLN cc_start: 0.7558 (mp10) cc_final: 0.7302 (mp10)
REVERT: A   41 LYS cc_start: 0.8293 (mtmm) cc_final: 0.7869 (ttpt)
REVERT: A  131 TYR cc_start: 0.8788 (t80) cc_final: 0.8472 (t80)
REVERT: A  164 ASN cc_start: 0.8925 (p0) cc_final: 0.8517 (p0)
REVERT: F  989 SER cc_start: 0.8674 (t) cc_final: 0.7992 (p)
REVERT: F 1087 MET cc_start: 0.8452 (ptm) cc_final: 0.8150 (ptm)
REVERT: B  131 TYR cc_start: 0.8753 (t80) cc_final: 0.8359 (t80)
REVERT: B  155 SER cc_start: 0.9213 (p) cc_final: 0.8968 (t)
REVERT: B  213 ARG cc_start: 0.8941 (mmm-85) cc_final: 0.8547 (mtp85)
REVERT: Z  992 GLN cc_start: 0.8916 (pm20) cc_final: 0.8352 (pm20)
REVERT: Z  994 GLU cc_start: 0.7517 (tt0) cc_final: 0.7248 (tt0)
REVERT: Z 1067 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7568 (mp10)
REVERT: C   21 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8450 (t70)
REVERT: C   32 ASP cc_start: 0.8521 (t70) cc_final: 0.8253 (t70)
  outliers start: 55
  outliers final: 46
  residues processed: 264
  average time/residue: 0.1266
  time to fit residues: 46.4174
Evaluate side-chains
  259 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 210
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue 1038 ARG
Chi-restraints excluded: chain J residue 1051 GLN
Chi-restraints excluded: chain J residue 1062 VAL
Chi-restraints excluded: chain J residue 1068 GLU
Chi-restraints excluded: chain J residue 1115 SER
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain F residue  998 VAL
Chi-restraints excluded: chain F residue 1000 THR
Chi-restraints excluded: chain F residue 1062 VAL
Chi-restraints excluded: chain F residue 1068 GLU
Chi-restraints excluded: chain F residue 1100 VAL
Chi-restraints excluded: chain F residue 1113 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  163 ASN
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain Z residue  972 THR
Chi-restraints excluded: chain Z residue  984 ILE
Chi-restraints excluded: chain Z residue  998 VAL
Chi-restraints excluded: chain Z residue 1000 THR
Chi-restraints excluded: chain Z residue 1060 LEU
Chi-restraints excluded: chain Z residue 1062 VAL
Chi-restraints excluded: chain Z residue 1068 GLU
Chi-restraints excluded: chain Z residue 1099 THR
Chi-restraints excluded: chain Z residue 1117 LEU
Chi-restraints excluded: chain Z residue 1119 VAL
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  172 ASN
Chi-restraints excluded: chain C residue  204 SER
Chi-restraints excluded: chain C residue  283 VAL
Chi-restraints excluded: chain C residue  345 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 124 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 120 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0870
   chunk 129 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.1162

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

Flipped N/Q/H residues before XYZ refinement:
J1106 ASN
A 123 GLN
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1106 ASN
** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z1106 ASN
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
C 250 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.112839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.092601 restraints weight = 17161.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.095465 restraints weight = 10210.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.097439 restraints weight = 7127.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.098772 restraints weight = 5519.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.099663 restraints weight = 4571.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12351  Z= 0.189
  Angle     :  0.610   8.801  16731  Z= 0.333
  Chirality :  0.045   0.276   1779
  Planarity :  0.003   0.029   2238
  Dihedral  :  4.634  21.167   1710
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.88 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 26.62 %
    Favored  : 68.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.22), residues: 1548
  helix: -2.75 (0.58), residues: 45
  sheet: -0.25 (0.20), residues: 813
  loop : -2.08 (0.22), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J1019 
 TYR   0.022   0.001   TYR C 149 
 PHE   0.022   0.002   PHE F1026 
 TRP   0.027   0.002   TRP C  56 
 HIS   0.004   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (12351)
  covalent geometry    : angle       0.61046 (16731)
  hydrogen bonds       : bond        0.02577 (  287)
  hydrogen bonds       : angle       5.26204 (  723)

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

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

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 217
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  992 GLN cc_start: 0.8578 (pm20) cc_final: 0.7943 (pm20)
REVERT: J 1038 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8211 (ttm-80)
REVERT: J 1051 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.7832 (tm-30)
REVERT: J 1067 GLN cc_start: 0.7582 (mp10) cc_final: 0.7329 (mp10)
REVERT: A   41 LYS cc_start: 0.8342 (mtmm) cc_final: 0.7913 (ttpt)
REVERT: A  131 TYR cc_start: 0.8813 (t80) cc_final: 0.8489 (t80)
REVERT: F  989 SER cc_start: 0.8707 (t) cc_final: 0.8030 (p)
REVERT: F 1067 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7580 (mp10)
REVERT: F 1087 MET cc_start: 0.8466 (ptm) cc_final: 0.8253 (ptm)
REVERT: B  131 TYR cc_start: 0.8766 (t80) cc_final: 0.8375 (t80)
REVERT: B  144 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8047 (m-40)
REVERT: B  155 SER cc_start: 0.9254 (p) cc_final: 0.8976 (t)
REVERT: B  213 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8499 (mtp85)
REVERT: B  238 TYR cc_start: 0.8159 (m-10) cc_final: 0.7908 (m-10)
REVERT: Z  983 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7242 (tm-30)
REVERT: Z  992 GLN cc_start: 0.8968 (pm20) cc_final: 0.8396 (pm20)
REVERT: Z  994 GLU cc_start: 0.7515 (tt0) cc_final: 0.7232 (tt0)
REVERT: Z 1067 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7577 (mp10)
REVERT: C   21 HIS cc_start: 0.8831 (OUTLIER) cc_final: 0.8398 (t70)
REVERT: C   32 ASP cc_start: 0.8633 (t70) cc_final: 0.8394 (t70)
  outliers start: 62
  outliers final: 54
  residues processed: 261
  average time/residue: 0.1113
  time to fit residues: 40.8651
Evaluate side-chains
  267 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 208
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  998 VAL
Chi-restraints excluded: chain J residue 1038 ARG
Chi-restraints excluded: chain J residue 1051 GLN
Chi-restraints excluded: chain J residue 1062 VAL
Chi-restraints excluded: chain J residue 1068 GLU
Chi-restraints excluded: chain J residue 1115 SER
Chi-restraints excluded: chain J residue 1126 THR
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain F residue  982 CYS
Chi-restraints excluded: chain F residue  998 VAL
Chi-restraints excluded: chain F residue 1000 THR
Chi-restraints excluded: chain F residue 1047 SER
Chi-restraints excluded: chain F residue 1062 VAL
Chi-restraints excluded: chain F residue 1068 GLU
Chi-restraints excluded: chain F residue 1100 VAL
Chi-restraints excluded: chain F residue 1113 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain Z residue  972 THR
Chi-restraints excluded: chain Z residue  983 GLN
Chi-restraints excluded: chain Z residue  984 ILE
Chi-restraints excluded: chain Z residue  998 VAL
Chi-restraints excluded: chain Z residue 1000 THR
Chi-restraints excluded: chain Z residue 1060 LEU
Chi-restraints excluded: chain Z residue 1062 VAL
Chi-restraints excluded: chain Z residue 1068 GLU
Chi-restraints excluded: chain Z residue 1099 THR
Chi-restraints excluded: chain Z residue 1117 LEU
Chi-restraints excluded: chain Z residue 1119 VAL
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  106 VAL
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  172 ASN
Chi-restraints excluded: chain C residue  196 SER
Chi-restraints excluded: chain C residue  204 SER
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  283 VAL
Chi-restraints excluded: chain C residue  345 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 113 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 23 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9980
   chunk 119 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   chunk 137 optimal weight:    0.0870
   chunk 105 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A 123 GLN
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 253 GLN
F1106 ASN
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 253 GLN
Z1106 ASN
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.121431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.101206 restraints weight = 16722.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.104382 restraints weight = 9457.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.106505 restraints weight = 6387.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.107989 restraints weight = 4810.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.108917 restraints weight = 3907.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12351  Z= 0.130
  Angle     :  0.585   9.204  16731  Z= 0.318
  Chirality :  0.044   0.277   1779
  Planarity :  0.003   0.029   2238
  Dihedral  :  4.527  27.225   1710
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 28.16 %
    Favored  : 68.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.22), residues: 1548
  helix: -2.49 (0.64), residues: 45
  sheet: -0.24 (0.20), residues: 819
  loop : -2.02 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG J1019 
 TYR   0.022   0.001   TYR C 184 
 PHE   0.019   0.001   PHE F1026 
 TRP   0.023   0.001   TRP C  56 
 HIS   0.005   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12351)
  covalent geometry    : angle       0.58525 (16731)
  hydrogen bonds       : bond        0.02295 (  287)
  hydrogen bonds       : angle       5.16723 (  723)

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

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

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3096 Ramachandran restraints generated.
    1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 226
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  992 GLN cc_start: 0.8552 (pm20) cc_final: 0.7906 (pm20)
REVERT: J 1051 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7775 (tm-30)
REVERT: J 1067 GLN cc_start: 0.7571 (mp10) cc_final: 0.7300 (mp10)
REVERT: A   41 LYS cc_start: 0.8288 (mtmm) cc_final: 0.7833 (ttpt)
REVERT: A  131 TYR cc_start: 0.8769 (t80) cc_final: 0.8459 (t80)
REVERT: A  164 ASN cc_start: 0.8878 (p0) cc_final: 0.8452 (p0)
REVERT: A  238 TYR cc_start: 0.8156 (m-80) cc_final: 0.7474 (m-80)
REVERT: F  989 SER cc_start: 0.8655 (t) cc_final: 0.7988 (p)
REVERT: F 1067 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7569 (mp10)
REVERT: B  131 TYR cc_start: 0.8693 (t80) cc_final: 0.8287 (t80)
REVERT: B  213 ARG cc_start: 0.8923 (mmm-85) cc_final: 0.8499 (mtp85)
REVERT: Z  992 GLN cc_start: 0.8969 (pm20) cc_final: 0.8394 (pm20)
REVERT: Z  994 GLU cc_start: 0.7487 (tt0) cc_final: 0.7221 (tt0)
REVERT: Z 1067 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7565 (mp10)
REVERT: C   21 HIS cc_start: 0.8790 (OUTLIER) cc_final: 0.8442 (t70)
REVERT: C   32 ASP cc_start: 0.8538 (t70) cc_final: 0.8307 (t70)
  outliers start: 47
  outliers final: 38
  residues processed: 260
  average time/residue: 0.1157
  time to fit residues: 42.4772
Evaluate side-chains
  250 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 210
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue 1051 GLN
Chi-restraints excluded: chain J residue 1062 VAL
Chi-restraints excluded: chain J residue 1115 SER
Chi-restraints excluded: chain J residue 1126 THR
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  279 LYS
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain F residue  998 VAL
Chi-restraints excluded: chain F residue 1000 THR
Chi-restraints excluded: chain F residue 1062 VAL
Chi-restraints excluded: chain F residue 1068 GLU
Chi-restraints excluded: chain F residue 1100 VAL
Chi-restraints excluded: chain F residue 1113 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain Z residue  972 THR
Chi-restraints excluded: chain Z residue  984 ILE
Chi-restraints excluded: chain Z residue  998 VAL
Chi-restraints excluded: chain Z residue 1000 THR
Chi-restraints excluded: chain Z residue 1060 LEU
Chi-restraints excluded: chain Z residue 1062 VAL
Chi-restraints excluded: chain Z residue 1068 GLU
Chi-restraints excluded: chain Z residue 1099 THR
Chi-restraints excluded: chain Z residue 1117 LEU
Chi-restraints excluded: chain Z residue 1119 VAL
Chi-restraints excluded: chain C residue   21 HIS
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  196 SER
Chi-restraints excluded: chain C residue  204 SER
Chi-restraints excluded: chain C residue  283 VAL
Chi-restraints excluded: chain C residue  345 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 48 optimal weight:    0.0870
   chunk 37 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 115 optimal weight:    0.8980
   chunk 152 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 128 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   overall best weight:    0.9960

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 123 GLN
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 309 ASN
F1106 ASN
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z1106 ASN
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.115205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.094559 restraints weight = 17154.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.097633 restraints weight = 9891.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.099741 restraints weight = 6762.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.101138 restraints weight = 5146.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.102104 restraints weight = 4224.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12351  Z= 0.174
  Angle     :  0.614   9.492  16731  Z= 0.332
  Chirality :  0.045   0.280   1779
  Planarity :  0.003   0.031   2238
  Dihedral  :  4.564  26.202   1710
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.56 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 28.01 %
    Favored  : 67.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.22), residues: 1548
  helix: -2.64 (0.60), residues: 45
  sheet: -0.23 (0.20), residues: 813
  loop : -2.03 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG J1061 
 TYR   0.021   0.001   TYR C 184 
 PHE   0.019   0.002   PHE Z1070 
 TRP   0.038   0.002   TRP A  56 
 HIS   0.004   0.001   HIS B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (12351)
  covalent geometry    : angle       0.61437 (16731)
  hydrogen bonds       : bond        0.02514 (  287)
  hydrogen bonds       : angle       5.20617 (  723)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1858.06 seconds
wall clock time: 33 minutes 5.77 seconds (1985.77 seconds total)