Starting phenix.real_space_refine
on Sat Aug 23 03:18:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dw3_27750/08_2025/8dw3_27750.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dw3_27750/08_2025/8dw3_27750.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dw3_27750/08_2025/8dw3_27750.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dw3_27750/08_2025/8dw3_27750.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dw3_27750/08_2025/8dw3_27750.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dw3_27750/08_2025/8dw3_27750.map"
  }
  resolution = 4.26
  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=   0.019
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      33      5.16       5
     C    5897      2.51       5
     N    1564      2.21       5
     O    1857      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9351
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1140
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 3, 'TRANS': 151}
    Chain: "B"
      Number of atoms: 1521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1521
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 10, 'TRANS': 181}
    Chain: "C"
      Number of atoms: 1624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1624
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201}
    Chain: "D"
      Number of atoms: 1715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1715
          Classifications: {'peptide': 228}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215}
    Chain: "H"
      Number of atoms: 1609
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 216, 1607
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 216, 1607
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1646
    Chain: "L"
      Number of atoms: 1703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1703
          Classifications: {'peptide': 219}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207}
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 2.59, per 1000 atoms: 0.28
  Number of scatterers: 9351
  At special positions: 0
  Unit cell: (82.062, 125.712, 174.6, 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      33     16.00
     O    1857      8.00
     N    1564      7.00
     C    5897      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  89 " distance=2.40
    Simple disulfide: pdb=" SG  CYS C 134 " - pdb=" SG  CYS C 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 154 " - pdb=" SG  CYS D 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.03

  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=1, symmetry=0
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG E   1 " - " ASN B 343 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 290.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2234

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 23 sheets defined
      15.3% alpha, 31.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 25
      removed outlier: 3.928A  pdb=" N   GLU A  20 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA A  24 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 35
    Processing helix  chain 'A' and resid 49 through 58
      removed outlier: 4.283A  pdb=" N   LEU A  53 " --> pdb=" O   THR A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 69
      removed outlier: 3.817A  pdb=" N   ASN A  69 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 91
      removed outlier: 3.930A  pdb=" N   LEU A  86 " --> pdb=" O   THR A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 103
      removed outlier: 3.747A  pdb=" N   GLU A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 123
      removed outlier: 3.610A  pdb=" N   LEU A 119 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   LEU A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 135
      removed outlier: 4.251A  pdb=" N   VAL A 129 " --> pdb=" O   HIS A 125 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLU A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASN A 135 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 156
      removed outlier: 3.938A  pdb=" N   ILE A 152 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ASN A 156 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 169
      removed outlier: 4.275A  pdb=" N   ALA A 162 " --> pdb=" O   ASN A 158 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE A 164 " --> pdb=" O   ASP A 160 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 343
      removed outlier: 3.543A  pdb=" N   PHE B 342 " --> pdb=" O   PHE B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.558A  pdb=" N   ALA B 352 " --> pdb=" O   SER B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 369
      removed outlier: 3.803A  pdb=" N   VAL B 367 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   TYR B 369 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 408
      removed outlier: 3.789A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
      removed outlier: 3.869A  pdb=" N   TYR B 421 " --> pdb=" O   LYS B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 506
      removed outlier: 3.640A  pdb=" N   GLN B 506 " --> pdb=" O   VAL B 503 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 126
      removed outlier: 3.606A  pdb=" N   LEU C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.724A  pdb=" N   SER D  31 " --> pdb=" O   PRO D  28 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   TYR D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 28 through 32'
    Processing helix  chain 'D' and resid 170 through 172
      No H-bonds generated for 'chain 'D' and resid 170 through 172'
    Processing helix  chain 'D' and resid 199 through 203
      removed outlier: 3.715A  pdb=" N   SER D 202 " --> pdb=" O   PRO D 199 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.602A  pdb=" N   THR H  31 " --> pdb=" O   GLY H  28 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 65
      removed outlier: 3.947A  pdb=" N   GLN H  65 " --> pdb=" O   PRO H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 65'
    Processing helix  chain 'H' and resid 191 through 193
      No H-bonds generated for 'chain 'H' and resid 191 through 193'
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.989A  pdb=" N   VAL L  89 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 127 through 134
    Processing helix  chain 'L' and resid 189 through 195
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 356
      removed outlier: 3.761A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5
      removed outlier: 3.914A  pdb=" N   ARG C  24 " --> pdb=" O   THR C   5 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 39
    Processing sheet with id=AA6, first strand: chain 'C' and resid 34 through 39
    Processing sheet with id=AA7, first strand: chain 'C' and resid 49 through 50
    Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 118
    Processing sheet with id=AA9, first strand: chain 'C' and resid 145 through 150
    Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 6
    Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.498A  pdb=" N   GLU D  10 " --> pdb=" O   THR D 124 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLY D  33 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   ILE D  34 " --> pdb=" O   TRP D  50 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   TRP D  50 " --> pdb=" O   ILE D  34 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   TRP D  36 " --> pdb=" O   MET D  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 138
    Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 138
    Processing sheet with id=AB5, first strand: chain 'D' and resid 165 through 168
      removed outlier: 4.150A  pdb=" N   TYR D 208 " --> pdb=" O   VAL D 225 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 2 through 5
    Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.734A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.734A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL H 108 " --> pdb=" O   GLY H  98 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 124 through 128
      removed outlier: 6.630A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL H 185 " --> pdb=" O   HIS H 168 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 155 through 158
      removed outlier: 4.121A  pdb=" N   TYR H 198 " --> pdb=" O   VAL H 215 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.570A  pdb=" N   THR L 108 " --> pdb=" O   TYR L  92 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'L' and resid 120 through 124
      removed outlier: 5.933A  pdb=" N   TYR L 179 " --> pdb=" O   ASN L 144 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'L' and resid 151 through 156

    336 hydrogen bonds defined for protein.
    864 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: 1.40

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        0.50 -     0.77: 1
        0.77 -     1.04: 0
        1.04 -     1.31: 1548
        1.31 -     1.58: 7967
        1.58 -     1.84: 46
  Bond restraints: 9562
  Sorted by residual:
  bond pdb=" CG  PRO D  28 "
       pdb=" CD  PRO D  28 "
    ideal  model  delta    sigma   weight residual
    1.503  0.505  0.998 3.40e-02 8.65e+02 8.62e+02
  bond pdb=" CG  PRO C 204 "
       pdb=" CD  PRO C 204 "
    ideal  model  delta    sigma   weight residual
    1.503  1.060  0.443 3.40e-02 8.65e+02 1.70e+02
  bond pdb=" N   PRO D  28 "
       pdb=" CD  PRO D  28 "
    ideal  model  delta    sigma   weight residual
    1.473  1.589 -0.116 1.40e-02 5.10e+03 6.84e+01
  bond pdb=" CB  PRO D  28 "
       pdb=" CG  PRO D  28 "
    ideal  model  delta    sigma   weight residual
    1.492  1.844 -0.352 5.00e-02 4.00e+02 4.95e+01
  bond pdb=" N   PRO C 204 "
       pdb=" CD  PRO C 204 "
    ideal  model  delta    sigma   weight residual
    1.473  1.569 -0.096 1.40e-02 5.10e+03 4.73e+01
  ... (remaining 9557 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.56: 12984
        7.56 -    15.11: 14
       15.11 -    22.67: 5
       22.67 -    30.23: 0
       30.23 -    37.79: 1
  Bond angle restraints: 13004
  Sorted by residual:
  angle pdb=" N   PRO D  28 "
        pdb=" CD  PRO D  28 "
        pdb=" CG  PRO D  28 "
      ideal   model   delta    sigma   weight residual
     103.20   65.41   37.79 1.50e+00 4.44e-01 6.35e+02
  angle pdb=" N   PRO C 204 "
        pdb=" CD  PRO C 204 "
        pdb=" CG  PRO C 204 "
      ideal   model   delta    sigma   weight residual
     103.20   81.48   21.72 1.50e+00 4.44e-01 2.10e+02
  angle pdb=" CA  PRO C 204 "
        pdb=" N   PRO C 204 "
        pdb=" CD  PRO C 204 "
      ideal   model   delta    sigma   weight residual
     112.00   94.26   17.74 1.40e+00 5.10e-01 1.61e+02
  angle pdb=" CA  PRO D  28 "
        pdb=" CB  PRO D  28 "
        pdb=" CG  PRO D  28 "
      ideal   model   delta    sigma   weight residual
     104.50   81.83   22.67 1.90e+00 2.77e-01 1.42e+02
  angle pdb=" CA  PRO C  81 "
        pdb=" N   PRO C  81 "
        pdb=" CD  PRO C  81 "
      ideal   model   delta    sigma   weight residual
     112.00   96.12   15.88 1.40e+00 5.10e-01 1.29e+02
  ... (remaining 12999 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.00: 5008
       21.00 -    42.01: 607
       42.01 -    63.01: 88
       63.01 -    84.01: 20
       84.01 -   105.02: 6
  Dihedral angle restraints: 5729
    sinusoidal: 2221
      harmonic: 3508
  Sorted by residual:
  dihedral pdb=" CB  CYS D 154 "
           pdb=" SG  CYS D 154 "
           pdb=" SG  CYS D 210 "
           pdb=" CB  CYS D 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.97   81.97     1      1.00e+01 1.00e-02 8.26e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   16.91   76.09     1      1.00e+01 1.00e-02 7.29e+01
  dihedral pdb=" CB  CYS C 134 "
           pdb=" SG  CYS C 134 "
           pdb=" SG  CYS C 194 "
           pdb=" CB  CYS C 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -161.05   75.05     1      1.00e+01 1.00e-02 7.12e+01
  ... (remaining 5726 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 1453
       0.131 -    0.263: 12
       0.263 -    0.394: 2
       0.394 -    0.525: 0
       0.525 -    0.657: 1
  Chirality restraints: 1468
  Sorted by residual:
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-02 2.50e+03 1.77e+02
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 343 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.74   -0.66 2.00e-01 2.50e+01 1.08e+01
  chirality pdb=" CA  TRP D  50 "
            pdb=" N   TRP D  50 "
            pdb=" C   TRP D  50 "
            pdb=" CB  TRP D  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.08e+00
  ... (remaining 1465 not shown)

  Planarity restraints: 1671
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   1 "   -0.081 2.00e-02 2.50e+03   6.71e-02 5.62e+01
        pdb=" C7  NAG E   1 "    0.020 2.00e-02 2.50e+03
        pdb=" C8  NAG E   1 "   -0.061 2.00e-02 2.50e+03
        pdb=" N2  NAG E   1 "    0.108 2.00e-02 2.50e+03
        pdb=" O7  NAG E   1 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 160 "    0.085 5.00e-02 4.00e+02   1.22e-01 2.39e+01
        pdb=" N   PRO D 161 "   -0.211 5.00e-02 4.00e+02
        pdb=" CA  PRO D 161 "    0.069 5.00e-02 4.00e+02
        pdb=" CD  PRO D 161 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D  50 "    0.034 2.00e-02 2.50e+03   3.08e-02 2.37e+01
        pdb=" CG  TRP D  50 "   -0.082 2.00e-02 2.50e+03
        pdb=" CD1 TRP D  50 "    0.039 2.00e-02 2.50e+03
        pdb=" CD2 TRP D  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP D  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D  50 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D  50 "    0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP D  50 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1668 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.66: 233
        2.66 -     3.22: 8587
        3.22 -     3.78: 13725
        3.78 -     4.34: 17656
        4.34 -     4.90: 29133
  Nonbonded interactions: 69334
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 345 "
            pdb=" OG  SER D 109 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" O   ILE C 106 "
            pdb=" OH  TYR C 140 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" O   SER C 121 "
            pdb=" NE2 GLN C 124 "
     model   vdw
     2.186 3.120
  nonbonded pdb=" OG  SER B 383 "
            pdb=" OG  SER H 100 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OG  SER D 202 "
            pdb=" OE1 GLN D 206 "
     model   vdw
     2.204 3.040
  ... (remaining 69329 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ 
 through 20 or resid 23 or resid 26 through 27 or resid 29 through 31 or resid 3 \ 
4 through 43 or resid 45 or resid 47 through 50 or resid 52 through 53 or resid  \ 
55 or resid 58 or resid 60 through 77 or resid 79 or resid 82 through 83 or resi \ 
d 85 through 91 or resid 94 or resid 97 through 99 or resid 101 through 213))
  selection = (chain 'L' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ 
 through 20 or resid 23 or resid 26 through 27 or resid 29 or resid 32 through 3 \ 
3 or resid 39 through 48 or resid 50 or resid 52 through 55 or resid 57 through  \ 
58 or resid 60 or resid 63 or resid 65 through 82 or resid 84 or resid 87 throug \ 
h 88 or resid 90 through 96 or resid 100 or resid 103 through 105 or resid 107 t \ 
hrough 219))
}

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=0.00 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:             1.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.870
  Find NCS groups from input model:        0.070
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
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      :  0.014   0.998   9578  Z= 0.646
  Angle     :  0.965  37.787  13037  Z= 0.532
  Chirality :  0.051   0.657   1468
  Planarity :  0.008   0.122   1670
  Dihedral  : 17.592 105.017   3459
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.71 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 37.69 %
    Favored  : 62.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.24), residues: 1209
  helix: -0.33 (0.49), residues: 104
  sheet:  0.37 (0.27), residues: 418
  loop : -1.29 (0.24), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 148 
 TYR   0.041   0.001   TYR L 102 
 PHE   0.025   0.001   PHE L 145 
 TRP   0.082   0.003   TRP D  50 
 HIS   0.005   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.01266 ( 9562)
  covalent geometry    : angle       0.94946 (13004)
  SS BOND              : bond        0.10592 (   12)
  SS BOND              : angle       3.49234 (   24)
  hydrogen bonds       : bond        0.14673 (  314)
  hydrogen bonds       : angle       6.46055 (  864)
  Misc. bond           : bond        0.46470 (    1)
  link_BETA1-4         : bond        0.00339 (    2)
  link_BETA1-4         : angle       2.06847 (    6)
  link_NAG-ASN         : bond        0.00913 (    1)
  link_NAG-ASN         : angle       6.00156 (    3)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 205
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8274 (mp) cc_final: 0.7734 (tp)
REVERT: B  489 TYR cc_start: 0.6882 (m-80) cc_final: 0.6449 (m-80)
REVERT: C  117 ILE cc_start: 0.9102 (tt) cc_final: 0.8880 (tt)
REVERT: C  154 LEU cc_start: 0.9124 (tp) cc_final: 0.8874 (pt)
REVERT: D   48 MET cc_start: 0.6484 (mmm) cc_final: 0.6169 (tpp)
REVERT: D  138 LEU cc_start: 0.7749 (tp) cc_final: 0.7006 (mp)
REVERT: D  168 TRP cc_start: 0.7187 (m100) cc_final: 0.6603 (m100)
REVERT: D  210 CYS cc_start: 0.4075 (t) cc_final: 0.2355 (t)
REVERT: H  158 TRP cc_start: 0.7154 (m100) cc_final: 0.6662 (m100)
  outliers start: 1
  outliers final: 1
  residues processed: 205
  average time/residue: 0.0929
  time to fit residues: 26.2745
Evaluate side-chains
  128 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:   30.0000
   chunk 117 optimal weight:    5.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 450 ASN
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 206 GLN
D 218 ASN
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 208 ASN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 172 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.068268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.052602 restraints weight = 70896.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.054260 restraints weight = 39489.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.055384 restraints weight = 26090.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.056175 restraints weight = 19235.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.056716 restraints weight = 15393.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.085   9578  Z= 0.290
  Angle     :  0.798   8.907  13037  Z= 0.405
  Chirality :  0.047   0.177   1468
  Planarity :  0.006   0.087   1670
  Dihedral  :  6.591  52.308   1372
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 16.97
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.53 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  6.78 %
    Favored  : 92.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.11 (0.24), residues: 1209
  helix: -0.48 (0.46), residues: 118
  sheet:  0.11 (0.26), residues: 437
  loop : -1.40 (0.24), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  60 
 TYR   0.021   0.002   TYR L  98 
 PHE   0.025   0.003   PHE C  98 
 TRP   0.032   0.002   TRP D  50 
 HIS   0.010   0.002   HIS H 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00652 ( 9562)
  covalent geometry    : angle       0.79060 (13004)
  SS BOND              : bond        0.01158 (   12)
  SS BOND              : angle       1.83812 (   24)
  hydrogen bonds       : bond        0.03601 (  314)
  hydrogen bonds       : angle       5.74364 (  864)
  Misc. bond           : bond        0.00528 (    1)
  link_BETA1-4         : bond        0.00348 (    2)
  link_BETA1-4         : angle       3.07841 (    6)
  link_NAG-ASN         : bond        0.00149 (    1)
  link_NAG-ASN         : angle       3.15176 (    3)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 152
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.9477 (mp) cc_final: 0.9114 (tp)
REVERT: B  386 LYS cc_start: 0.9032 (mtpp) cc_final: 0.8695 (mtpt)
REVERT: B  390 LEU cc_start: 0.8529 (pp) cc_final: 0.8257 (pp)
REVERT: B  414 GLN cc_start: 0.8255 (tt0) cc_final: 0.7828 (tm-30)
REVERT: B  456 PHE cc_start: 0.6707 (t80) cc_final: 0.6353 (t80)
REVERT: B  489 TYR cc_start: 0.7238 (m-80) cc_final: 0.7010 (m-80)
REVERT: C  118 PHE cc_start: 0.8199 (m-80) cc_final: 0.7435 (m-80)
REVERT: D   48 MET cc_start: 0.8659 (mmm) cc_final: 0.8063 (tpp)
REVERT: D   87 ARG cc_start: 0.8711 (mpp-170) cc_final: 0.8258 (mtt90)
REVERT: D   94 TYR cc_start: 0.9022 (m-10) cc_final: 0.8586 (m-80)
REVERT: D  108 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8286 (mp0)
REVERT: D  168 TRP cc_start: 0.7872 (m100) cc_final: 0.6969 (m100)
REVERT: D  210 CYS cc_start: 0.7792 (t) cc_final: 0.5693 (t)
REVERT: H   37 VAL cc_start: 0.9586 (t) cc_final: 0.9287 (p)
REVERT: H   48 MET cc_start: 0.8854 (mpp) cc_final: 0.8599 (mpp)
REVERT: H  149 TYR cc_start: 0.5464 (p90) cc_final: 0.5170 (p90)
REVERT: H  158 TRP cc_start: 0.7552 (m100) cc_final: 0.7109 (m100)
  outliers start: 5
  outliers final: 2
  residues processed: 157
  average time/residue: 0.0739
  time to fit residues: 16.9773
Evaluate side-chains
  90 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    6.9990
   chunk 92 optimal weight:    8.9990
   chunk 35 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 89 optimal weight:    8.9990
   chunk 112 optimal weight:    0.9980
   chunk 50 optimal weight:    8.9990
   chunk 47 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 110 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    5.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  52 HIS
** A  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 116 ASN
D 218 ASN
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 130 GLN
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.066110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.050754 restraints weight = 68451.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.052343 restraints weight = 38342.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.053419 restraints weight = 25522.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.054183 restraints weight = 19049.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.054699 restraints weight = 15343.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3093
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3093
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.4076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   9578  Z= 0.264
  Angle     :  0.733   8.858  13037  Z= 0.373
  Chirality :  0.046   0.172   1468
  Planarity :  0.006   0.063   1670
  Dihedral  :  5.951  32.588   1372
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 17.24
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.11 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  6.30 %
    Favored  : 93.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.24), residues: 1209
  helix: -0.63 (0.45), residues: 119
  sheet: -0.07 (0.25), residues: 426
  loop : -1.46 (0.24), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  81 
 TYR   0.022   0.002   TYR D 190 
 PHE   0.020   0.002   PHE B 456 
 TRP   0.017   0.002   TRP D 105 
 HIS   0.009   0.002   HIS H 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 ( 9562)
  covalent geometry    : angle       0.72448 (13004)
  SS BOND              : bond        0.00629 (   12)
  SS BOND              : angle       1.92507 (   24)
  hydrogen bonds       : bond        0.03431 (  314)
  hydrogen bonds       : angle       5.67618 (  864)
  Misc. bond           : bond        0.00201 (    1)
  link_BETA1-4         : bond        0.00134 (    2)
  link_BETA1-4         : angle       2.89478 (    6)
  link_NAG-ASN         : bond        0.00182 (    1)
  link_NAG-ASN         : angle       3.39727 (    3)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 131
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  390 LEU cc_start: 0.8641 (pp) cc_final: 0.8388 (pp)
REVERT: B  458 LYS cc_start: 0.8650 (mttt) cc_final: 0.8149 (mmtt)
REVERT: B  516 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7709 (tm-30)
REVERT: D   81 MET cc_start: 0.8795 (tmm) cc_final: 0.8594 (tmm)
REVERT: D  108 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8802 (mp0)
REVERT: D  168 TRP cc_start: 0.7918 (m100) cc_final: 0.6731 (m100)
REVERT: D  210 CYS cc_start: 0.7930 (t) cc_final: 0.6274 (t)
REVERT: H   10 GLU cc_start: 0.8089 (tp30) cc_final: 0.7620 (tp30)
REVERT: H   83 TRP cc_start: 0.8172 (m100) cc_final: 0.7528 (m100)
REVERT: H  158 TRP cc_start: 0.7653 (m100) cc_final: 0.7236 (m100)
REVERT: L  102 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.5490 (m-80)
REVERT: L  130 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8099 (tp-100)
  outliers start: 4
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0820
  time to fit residues: 16.0041
Evaluate side-chains
  81 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 101 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 24 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 99 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
** A  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 218 ASN
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.066229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.050878 restraints weight = 71355.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.052472 restraints weight = 39843.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.053615 restraints weight = 26533.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.054377 restraints weight = 19532.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.054896 restraints weight = 15641.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3096
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.4382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9578  Z= 0.199
  Angle     :  0.679   9.678  13037  Z= 0.340
  Chirality :  0.045   0.207   1468
  Planarity :  0.005   0.059   1670
  Dihedral  :  5.580  33.896   1372
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.20 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.22 (0.24), residues: 1209
  helix: -0.41 (0.45), residues: 118
  sheet: -0.06 (0.25), residues: 423
  loop : -1.40 (0.25), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG H  59 
 TYR   0.021   0.002   TYR D 190 
 PHE   0.017   0.002   PHE B 456 
 TRP   0.011   0.002   TRP H  33 
 HIS   0.008   0.001   HIS H 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 9562)
  covalent geometry    : angle       0.66835 (13004)
  SS BOND              : bond        0.00491 (   12)
  SS BOND              : angle       1.65646 (   24)
  hydrogen bonds       : bond        0.02922 (  314)
  hydrogen bonds       : angle       5.57898 (  864)
  Misc. bond           : bond        0.00047 (    1)
  link_BETA1-4         : bond        0.00226 (    2)
  link_BETA1-4         : angle       3.11273 (    6)
  link_NAG-ASN         : bond        0.00274 (    1)
  link_NAG-ASN         : angle       5.18831 (    3)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 GLU cc_start: 0.9399 (tp30) cc_final: 0.8716 (pt0)
REVERT: B  390 LEU cc_start: 0.8581 (pp) cc_final: 0.8341 (pp)
REVERT: B  458 LYS cc_start: 0.8709 (mttt) cc_final: 0.8142 (mmtt)
REVERT: D   81 MET cc_start: 0.8871 (tmm) cc_final: 0.8628 (tmm)
REVERT: D  168 TRP cc_start: 0.7942 (m100) cc_final: 0.6790 (m100)
REVERT: D  210 CYS cc_start: 0.7967 (t) cc_final: 0.6271 (t)
REVERT: H   10 GLU cc_start: 0.8194 (tp30) cc_final: 0.7702 (tp30)
REVERT: H   83 TRP cc_start: 0.8196 (m100) cc_final: 0.7117 (m100)
REVERT: H  158 TRP cc_start: 0.7717 (m100) cc_final: 0.7297 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0735
  time to fit residues: 13.5235
Evaluate side-chains
  81 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 116 optimal weight:   10.0000
   chunk 101 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   chunk 92 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0770
   chunk 18 optimal weight:    0.3980
   chunk 89 optimal weight:    9.9990
   overall best weight:    3.2944

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 116 ASN
D 206 GLN
D 214 HIS
H  82 GLN
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.066533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.051812 restraints weight = 58791.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.053286 restraints weight = 34586.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.054281 restraints weight = 23554.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.054917 restraints weight = 17858.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.055397 restraints weight = 14730.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3111
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.4565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9578  Z= 0.161
  Angle     :  0.653  10.105  13037  Z= 0.324
  Chirality :  0.045   0.149   1468
  Planarity :  0.005   0.056   1670
  Dihedral  :  5.443  31.615   1372
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.95 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.91 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.24), residues: 1209
  helix: -0.08 (0.48), residues: 113
  sheet: -0.08 (0.25), residues: 427
  loop : -1.33 (0.25), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  98 
 TYR   0.026   0.002   TYR H 180 
 PHE   0.020   0.002   PHE D 114 
 TRP   0.016   0.001   TRP H  33 
 HIS   0.005   0.001   HIS H 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 9562)
  covalent geometry    : angle       0.63891 (13004)
  SS BOND              : bond        0.00416 (   12)
  SS BOND              : angle       1.49740 (   24)
  hydrogen bonds       : bond        0.02749 (  314)
  hydrogen bonds       : angle       5.43377 (  864)
  Misc. bond           : bond        0.00033 (    1)
  link_BETA1-4         : bond        0.00487 (    2)
  link_BETA1-4         : angle       3.12943 (    6)
  link_NAG-ASN         : bond        0.00642 (    1)
  link_NAG-ASN         : angle       6.75798 (    3)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 GLU cc_start: 0.9372 (tp30) cc_final: 0.8683 (pt0)
REVERT: B  390 LEU cc_start: 0.8569 (pp) cc_final: 0.8324 (pp)
REVERT: B  458 LYS cc_start: 0.8722 (mttt) cc_final: 0.8141 (mmtt)
REVERT: D    3 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7873 (tm-30)
REVERT: D  108 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8895 (mp0)
REVERT: D  168 TRP cc_start: 0.7941 (m100) cc_final: 0.6784 (m100)
REVERT: D  206 GLN cc_start: 0.5134 (OUTLIER) cc_final: 0.4879 (pp30)
REVERT: D  210 CYS cc_start: 0.7936 (t) cc_final: 0.6129 (t)
REVERT: H   10 GLU cc_start: 0.8181 (tp30) cc_final: 0.7713 (tp30)
REVERT: H  158 TRP cc_start: 0.7724 (m100) cc_final: 0.7315 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0882
  time to fit residues: 15.7553
Evaluate side-chains
  85 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0970
   chunk 90 optimal weight:    6.9990
   chunk 96 optimal weight:   10.0000
   chunk 69 optimal weight:    0.5980
   chunk 39 optimal weight:    8.9990
   overall best weight:    2.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 218 ASN
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.066602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.051844 restraints weight = 58924.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.053298 restraints weight = 34776.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.054271 restraints weight = 23793.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.054969 restraints weight = 18105.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.055447 restraints weight = 14783.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.4685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9578  Z= 0.142
  Angle     :  0.652  10.399  13037  Z= 0.318
  Chirality :  0.044   0.164   1468
  Planarity :  0.004   0.054   1670
  Dihedral  :  5.281  33.291   1372
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.78 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.02 (0.25), residues: 1209
  helix: -0.00 (0.48), residues: 113
  sheet:  0.02 (0.25), residues: 440
  loop : -1.30 (0.25), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  59 
 TYR   0.021   0.001   TYR H 180 
 PHE   0.013   0.002   PHE C  72 
 TRP   0.015   0.001   TRP D  50 
 HIS   0.004   0.001   HIS H 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9562)
  covalent geometry    : angle       0.63466 (13004)
  SS BOND              : bond        0.00344 (   12)
  SS BOND              : angle       1.39141 (   24)
  hydrogen bonds       : bond        0.02705 (  314)
  hydrogen bonds       : angle       5.29814 (  864)
  Misc. bond           : bond        0.00026 (    1)
  link_BETA1-4         : bond        0.00331 (    2)
  link_BETA1-4         : angle       3.12526 (    6)
  link_NAG-ASN         : bond        0.01572 (    1)
  link_NAG-ASN         : angle       8.19974 (    3)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 GLU cc_start: 0.9342 (tp30) cc_final: 0.8650 (pt0)
REVERT: B  390 LEU cc_start: 0.8659 (pp) cc_final: 0.8326 (pp)
REVERT: B  458 LYS cc_start: 0.8724 (mttt) cc_final: 0.8011 (mmtm)
REVERT: D   48 MET cc_start: 0.8052 (mmt) cc_final: 0.7792 (mmt)
REVERT: D   81 MET cc_start: 0.8927 (tmm) cc_final: 0.8561 (tmm)
REVERT: D  108 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8949 (mp0)
REVERT: D  168 TRP cc_start: 0.7935 (m100) cc_final: 0.6867 (m100)
REVERT: D  210 CYS cc_start: 0.7918 (t) cc_final: 0.5920 (t)
REVERT: H   10 GLU cc_start: 0.8227 (tp30) cc_final: 0.7711 (tp30)
REVERT: H   83 TRP cc_start: 0.7817 (m100) cc_final: 0.6944 (m100)
REVERT: H  158 TRP cc_start: 0.7758 (m100) cc_final: 0.7379 (m100)
REVERT: H  180 TYR cc_start: 0.8971 (m-10) cc_final: 0.8742 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0864
  time to fit residues: 16.3184
Evaluate side-chains
  83 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 93 optimal weight:    8.9990
   chunk 64 optimal weight:   10.0000
   chunk 85 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 117 optimal weight:    3.9990
   chunk 58 optimal weight:    8.9990
   chunk 105 optimal weight:   10.0000
   chunk 101 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 70 optimal weight:   20.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.065777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.050717 restraints weight = 70052.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.052297 restraints weight = 39517.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.053379 restraints weight = 26359.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.054107 restraints weight = 19568.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.054608 restraints weight = 15762.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3094
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.4905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9578  Z= 0.179
  Angle     :  0.662  13.555  13037  Z= 0.327
  Chirality :  0.045   0.160   1468
  Planarity :  0.004   0.055   1670
  Dihedral  :  5.177  28.587   1372
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.53 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.24), residues: 1209
  helix:  0.07 (0.48), residues: 113
  sheet:  0.07 (0.25), residues: 429
  loop : -1.31 (0.25), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 217 
 TYR   0.021   0.002   TYR H  52 
 PHE   0.017   0.002   PHE H 170 
 TRP   0.014   0.001   TRP H  33 
 HIS   0.006   0.001   HIS H 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 9562)
  covalent geometry    : angle       0.65218 (13004)
  SS BOND              : bond        0.00447 (   12)
  SS BOND              : angle       1.44712 (   24)
  hydrogen bonds       : bond        0.02838 (  314)
  hydrogen bonds       : angle       5.37273 (  864)
  Misc. bond           : bond        0.00048 (    1)
  link_BETA1-4         : bond        0.00458 (    2)
  link_BETA1-4         : angle       2.75876 (    6)
  link_NAG-ASN         : bond        0.00474 (    1)
  link_NAG-ASN         : angle       5.47742 (    3)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 GLU cc_start: 0.9339 (tp30) cc_final: 0.8658 (pt0)
REVERT: A  102 ASN cc_start: 0.8818 (p0) cc_final: 0.8602 (p0)
REVERT: B  390 LEU cc_start: 0.8701 (pp) cc_final: 0.8371 (pp)
REVERT: B  458 LYS cc_start: 0.8691 (mttt) cc_final: 0.8111 (mmtt)
REVERT: D    3 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8046 (tm-30)
REVERT: D   48 MET cc_start: 0.8135 (mmt) cc_final: 0.7452 (mmt)
REVERT: D   81 MET cc_start: 0.8924 (tmm) cc_final: 0.8626 (tmm)
REVERT: D  108 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8982 (mp0)
REVERT: D  168 TRP cc_start: 0.7907 (m100) cc_final: 0.6791 (m100)
REVERT: D  210 CYS cc_start: 0.7886 (t) cc_final: 0.5871 (t)
REVERT: H   10 GLU cc_start: 0.8245 (tp30) cc_final: 0.7719 (tp30)
REVERT: H   83 TRP cc_start: 0.7920 (m100) cc_final: 0.7020 (m100)
REVERT: H  158 TRP cc_start: 0.7720 (m100) cc_final: 0.7340 (m100)
REVERT: H  180 TYR cc_start: 0.8999 (m-10) cc_final: 0.8766 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0900
  time to fit residues: 15.6824
Evaluate side-chains
  86 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 96 optimal weight:    9.9990
   chunk 73 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 67 optimal weight:    8.9990
   chunk 43 optimal weight:    4.9990
   chunk 89 optimal weight:   10.0000
   chunk 14 optimal weight:   20.0000
   chunk 13 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   overall best weight:    2.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 218 ASN
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.066685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.051414 restraints weight = 70535.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.053070 restraints weight = 39192.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.054153 restraints weight = 25873.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.054944 restraints weight = 19164.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.055472 restraints weight = 15314.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3118
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3118
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.4998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9578  Z= 0.128
  Angle     :  0.669  13.570  13037  Z= 0.321
  Chirality :  0.045   0.224   1468
  Planarity :  0.004   0.055   1670
  Dihedral  :  5.176  35.024   1372
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.29 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.25), residues: 1209
  helix:  0.13 (0.49), residues: 113
  sheet:  0.15 (0.25), residues: 429
  loop : -1.25 (0.25), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  87 
 TYR   0.024   0.001   TYR L 102 
 PHE   0.014   0.002   PHE C  72 
 TRP   0.017   0.001   TRP H  33 
 HIS   0.003   0.001   HIS H 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9562)
  covalent geometry    : angle       0.63690 (13004)
  SS BOND              : bond        0.00387 (   12)
  SS BOND              : angle       1.35525 (   24)
  hydrogen bonds       : bond        0.02638 (  314)
  hydrogen bonds       : angle       5.22056 (  864)
  Misc. bond           : bond        0.00036 (    1)
  link_BETA1-4         : bond        0.00888 (    2)
  link_BETA1-4         : angle       3.28083 (    6)
  link_NAG-ASN         : bond        0.00260 (    1)
  link_NAG-ASN         : angle      12.21999 (    3)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 GLU cc_start: 0.9424 (tp30) cc_final: 0.8762 (pt0)
REVERT: A  102 ASN cc_start: 0.8830 (p0) cc_final: 0.8594 (p0)
REVERT: B  390 LEU cc_start: 0.8656 (pp) cc_final: 0.8333 (pp)
REVERT: B  458 LYS cc_start: 0.8695 (mttt) cc_final: 0.8023 (mmtm)
REVERT: D    3 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8154 (tm-30)
REVERT: D   81 MET cc_start: 0.8952 (tmm) cc_final: 0.8677 (tmm)
REVERT: D  108 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8999 (mp0)
REVERT: D  168 TRP cc_start: 0.7851 (m100) cc_final: 0.6877 (m100)
REVERT: D  210 CYS cc_start: 0.7886 (t) cc_final: 0.5658 (t)
REVERT: H   10 GLU cc_start: 0.8278 (tp30) cc_final: 0.7864 (tp30)
REVERT: H   12 LYS cc_start: 0.7974 (tptp) cc_final: 0.7546 (tptp)
REVERT: H   16 GLU cc_start: 0.8994 (mp0) cc_final: 0.8655 (mp0)
REVERT: H   83 TRP cc_start: 0.7887 (m100) cc_final: 0.6856 (m100)
REVERT: H  158 TRP cc_start: 0.7729 (m100) cc_final: 0.7354 (m100)
REVERT: H  180 TYR cc_start: 0.8936 (m-10) cc_final: 0.8672 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0839
  time to fit residues: 15.9313
Evaluate side-chains
  90 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   chunk 3 optimal weight:   40.0000
   chunk 105 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.064868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.049925 restraints weight = 69901.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.051504 restraints weight = 39411.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.052574 restraints weight = 26258.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.053317 restraints weight = 19488.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.053819 restraints weight = 15677.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.5215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9578  Z= 0.210
  Angle     :  0.705  13.936  13037  Z= 0.347
  Chirality :  0.046   0.232   1468
  Planarity :  0.005   0.060   1670
  Dihedral  :  5.374  34.273   1372
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.69 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.25), residues: 1209
  helix:  0.08 (0.47), residues: 113
  sheet: -0.05 (0.25), residues: 434
  loop : -1.26 (0.25), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  87 
 TYR   0.026   0.002   TYR L 102 
 PHE   0.017   0.002   PHE C  72 
 TRP   0.014   0.002   TRP H  33 
 HIS   0.006   0.001   HIS H 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 9562)
  covalent geometry    : angle       0.68119 (13004)
  SS BOND              : bond        0.00483 (   12)
  SS BOND              : angle       1.73296 (   24)
  hydrogen bonds       : bond        0.03003 (  314)
  hydrogen bonds       : angle       5.39165 (  864)
  Misc. bond           : bond        0.00092 (    1)
  link_BETA1-4         : bond        0.00487 (    2)
  link_BETA1-4         : angle       3.05554 (    6)
  link_NAG-ASN         : bond        0.00479 (    1)
  link_NAG-ASN         : angle      10.20429 (    3)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 GLU cc_start: 0.9383 (tp30) cc_final: 0.8774 (pt0)
REVERT: A  102 ASN cc_start: 0.8847 (p0) cc_final: 0.8614 (p0)
REVERT: B  386 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8442 (ptmt)
REVERT: B  390 LEU cc_start: 0.8679 (pp) cc_final: 0.8340 (pp)
REVERT: B  458 LYS cc_start: 0.8713 (mttt) cc_final: 0.8109 (mmtt)
REVERT: D    3 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7958 (tm-30)
REVERT: D   48 MET cc_start: 0.8396 (mmp) cc_final: 0.8102 (mmt)
REVERT: D  168 TRP cc_start: 0.7877 (m100) cc_final: 0.6771 (m100)
REVERT: D  210 CYS cc_start: 0.7942 (t) cc_final: 0.5906 (t)
REVERT: H   10 GLU cc_start: 0.8349 (tp30) cc_final: 0.7915 (tp30)
REVERT: H   83 TRP cc_start: 0.8041 (m100) cc_final: 0.7070 (m100)
REVERT: H  158 TRP cc_start: 0.7716 (m100) cc_final: 0.7357 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0825
  time to fit residues: 14.5190
Evaluate side-chains
  82 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 82 optimal weight:    0.0170
   chunk 108 optimal weight:   10.0000
   chunk 118 optimal weight:   10.0000
   chunk 54 optimal weight:   20.0000
   chunk 1 optimal weight:    0.8980
   chunk 26 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 47 optimal weight:    9.9990
   chunk 95 optimal weight:    8.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.3822

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  92 HIS
** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 218 ASN
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.066678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.051411 restraints weight = 70042.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.053099 restraints weight = 38595.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.054249 restraints weight = 25264.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.054961 restraints weight = 18548.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.055562 restraints weight = 14940.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.5214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9578  Z= 0.118
  Angle     :  0.675  13.629  13037  Z= 0.327
  Chirality :  0.046   0.223   1468
  Planarity :  0.004   0.054   1670
  Dihedral  :  5.101  33.677   1372
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.12 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.25), residues: 1209
  helix:  0.13 (0.50), residues: 108
  sheet:  0.01 (0.25), residues: 440
  loop : -1.17 (0.25), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  87 
 TYR   0.020   0.001   TYR H 180 
 PHE   0.015   0.001   PHE C  72 
 TRP   0.019   0.001   TRP H  33 
 HIS   0.012   0.001   HIS A 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9562)
  covalent geometry    : angle       0.65452 (13004)
  SS BOND              : bond        0.00308 (   12)
  SS BOND              : angle       1.41896 (   24)
  hydrogen bonds       : bond        0.02647 (  314)
  hydrogen bonds       : angle       5.21916 (  864)
  Misc. bond           : bond        0.00006 (    1)
  link_BETA1-4         : bond        0.00700 (    2)
  link_BETA1-4         : angle       3.14012 (    6)
  link_NAG-ASN         : bond        0.00166 (    1)
  link_NAG-ASN         : angle       9.40531 (    3)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 GLU cc_start: 0.9376 (tp30) cc_final: 0.8773 (pt0)
REVERT: A  102 ASN cc_start: 0.8891 (p0) cc_final: 0.8653 (p0)
REVERT: B  386 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8453 (ptmt)
REVERT: B  390 LEU cc_start: 0.8622 (pp) cc_final: 0.8309 (pp)
REVERT: B  458 LYS cc_start: 0.8690 (mttt) cc_final: 0.8089 (mmtt)
REVERT: D    3 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8010 (tm-30)
REVERT: D   48 MET cc_start: 0.8236 (mmp) cc_final: 0.7956 (mmt)
REVERT: D  168 TRP cc_start: 0.7825 (m100) cc_final: 0.6950 (m100)
REVERT: D  210 CYS cc_start: 0.7717 (t) cc_final: 0.5477 (t)
REVERT: H   10 GLU cc_start: 0.8349 (tp30) cc_final: 0.7978 (tp30)
REVERT: H   16 GLU cc_start: 0.8962 (mp0) cc_final: 0.8601 (mp0)
REVERT: H   83 TRP cc_start: 0.7810 (m100) cc_final: 0.6943 (m100)
REVERT: H  158 TRP cc_start: 0.7668 (m100) cc_final: 0.7311 (m100)
REVERT: L  124 PHE cc_start: 0.7779 (m-80) cc_final: 0.7507 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0747
  time to fit residues: 14.1807
Evaluate side-chains
  89 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 79 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 83 optimal weight:    0.0030
   chunk 47 optimal weight:    6.9990
   chunk 114 optimal weight:    2.9990
   chunk 67 optimal weight:    9.9990
   chunk 107 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9990
   chunk 56 optimal weight:   20.0000
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.9998

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.066636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.051575 restraints weight = 66774.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.053229 restraints weight = 36579.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.054349 restraints weight = 23899.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.055113 restraints weight = 17558.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.055604 restraints weight = 14019.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3125
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.5274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9578  Z= 0.126
  Angle     :  0.660  13.351  13037  Z= 0.319
  Chirality :  0.045   0.224   1468
  Planarity :  0.004   0.055   1670
  Dihedral  :  4.942  32.681   1372
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.62 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.25), residues: 1209
  helix:  0.00 (0.50), residues: 108
  sheet:  0.01 (0.25), residues: 438
  loop : -1.14 (0.25), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 509 
 TYR   0.022   0.001   TYR H  52 
 PHE   0.013   0.001   PHE C  72 
 TRP   0.017   0.001   TRP H  33 
 HIS   0.005   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9562)
  covalent geometry    : angle       0.64219 (13004)
  SS BOND              : bond        0.00341 (   12)
  SS BOND              : angle       1.42891 (   24)
  hydrogen bonds       : bond        0.02592 (  314)
  hydrogen bonds       : angle       5.16806 (  864)
  Misc. bond           : bond        0.00026 (    1)
  link_BETA1-4         : bond        0.00796 (    2)
  link_BETA1-4         : angle       2.98535 (    6)
  link_NAG-ASN         : bond        0.00216 (    1)
  link_NAG-ASN         : angle       8.50058 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1783.38 seconds
wall clock time: 31 minutes 36.79 seconds (1896.79 seconds total)