Starting phenix.real_space_refine
on Tue Mar  3 16:42:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n64_24193/03_2026/7n64_24193.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n64_24193/03_2026/7n64_24193.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n64_24193/03_2026/7n64_24193.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n64_24193/03_2026/7n64_24193.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n64_24193/03_2026/7n64_24193.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n64_24193/03_2026/7n64_24193.map"
  }
  resolution = 4.2
  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=   0.000 sd=   0.002
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      26      5.16       5
     C    4574      2.51       5
     N    1194      2.21       5
     O    1395      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7189
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2235
          Classifications: {'peptide': 277}
          Link IDs: {'PTRANS': 14, 'TRANS': 262}
    Chain: "B"
      Number of atoms: 1568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1568
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 11, 'TRANS': 186}
    Chain: "H"
      Number of atoms: 1687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1687
          Classifications: {'peptide': 222}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 209}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1604
          Classifications: {'peptide': 209}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197}
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      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
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.60, per 1000 atoms: 0.22
  Number of scatterers: 7189
  At special positions: 0
  Unit cell: (99, 79.2, 120.45, 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      26     16.00
     O    1395      8.00
     N    1194      7.00
     C    4574      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.02
    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 H  22 " - pdb=" SG  CYS H  94 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 160 " - pdb=" SG  CYS H 216 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
    NAG-ASN
      " NAG A1301 " - " ASN A  17 "
      " NAG A1302 " - " ASN A 165 "
      " NAG F   1 " - " ASN A 122 "
      " NAG G   1 " - " ASN B 343 "
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 270.6 milliseconds
  

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1680

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 17 sheets defined
      6.3% alpha, 28.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 364 through 370
      removed outlier: 3.708A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 390
    Processing helix  chain 'B' and resid 405 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 502 through 505
    Processing helix  chain 'H' and resid 59 through 63
      removed outlier: 3.853A  pdb=" N   LYS H  63 " --> pdb=" O   ASP H  60 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 205 through 209
    Processing helix  chain 'L' and resid 121 through 127
    Processing helix  chain 'L' and resid 183 through 187
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30
      removed outlier: 8.300A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   PHE A 201 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   ASP A 228 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85
    Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104
      removed outlier: 7.424A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   ALA A 243 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121
      removed outlier: 4.168A  pdb=" N   GLU A 132 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ASN A 164 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   SER A 162 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 121
    Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.779A  pdb=" N   SER B 514 " --> pdb=" O   TYR B 396 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA9, first strand: chain 'B' and resid 473 through 474
      removed outlier: 3.685A  pdb=" N   TYR B 473 " --> pdb=" O   TYR B 489 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   TYR B 489 " --> pdb=" O   TYR B 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'H' and resid 18 through 19
      removed outlier: 4.087A  pdb=" N   SER H  69 " --> pdb=" O   TYR H  78 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 47 through 50
      removed outlier: 5.264A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   TYR H  92 " --> pdb=" O   THR H 123 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 136 through 140
      removed outlier: 3.506A  pdb=" N   LYS H 163 " --> pdb=" O   SER H 136 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   TYR H 196 " --> pdb=" O   ASP H 164 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   SER H 199 " --> pdb=" O   PHE H 186 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 171 through 174
      removed outlier: 3.833A  pdb=" N   TYR H 214 " --> pdb=" O   VAL H 231 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AB6, first strand: chain 'L' and resid 45 through 46
      removed outlier: 3.581A  pdb=" N   GLN L  37 " --> pdb=" O   LYS L  45 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   THR L  85 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 114 through 118
      removed outlier: 4.729A  pdb=" N   SER L 131 " --> pdb=" O   LEU L 181 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   LEU L 181 " --> pdb=" O   SER L 131 " (cutoff:3.500A)
      removed outlier: 5.603A  pdb=" N   VAL L 133 " --> pdb=" O   LEU L 179 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   LEU L 179 " --> pdb=" O   VAL L 133 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   LEU L 135 " --> pdb=" O   SER L 177 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   SER L 177 " --> pdb=" O   LEU L 135 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   ASN L 137 " --> pdb=" O   LEU L 175 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LEU L 175 " --> pdb=" O   ASN L 137 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   PHE L 139 " --> pdb=" O   TYR L 173 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 144 through 149

    187 hydrogen bonds defined for protein.
    444 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.96

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1932
        1.33 -     1.45: 1675
        1.45 -     1.57: 3736
        1.57 -     1.70: 0
        1.70 -     1.82: 32
  Bond restraints: 7375
  Sorted by residual:
  bond pdb=" N   GLN L   3 "
       pdb=" CA  GLN L   3 "
    ideal  model  delta    sigma   weight residual
    1.452  1.504 -0.051 1.22e-02 6.72e+03 1.76e+01
  bond pdb=" C   ALA L 111 "
       pdb=" N   ALA L 112 "
    ideal  model  delta    sigma   weight residual
    1.333  1.240  0.093 2.74e-02 1.33e+03 1.14e+01
  bond pdb=" N   GLN L 100 "
       pdb=" CA  GLN L 100 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.17e-02 7.31e+03 9.83e+00
  bond pdb=" C   ALA B 520 "
       pdb=" N   PRO B 521 "
    ideal  model  delta    sigma   weight residual
    1.331  1.369 -0.038 1.27e-02 6.20e+03 9.03e+00
  bond pdb=" N   ARG A 237 "
       pdb=" CA  ARG A 237 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.13e-02 7.83e+03 8.78e+00
  ... (remaining 7370 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 9485
        2.24 -     4.48: 497
        4.48 -     6.72: 44
        6.72 -     8.97: 7
        8.97 -    11.21: 2
  Bond angle restraints: 10035
  Sorted by residual:
  angle pdb=" CA  ALA B 520 "
        pdb=" C   ALA B 520 "
        pdb=" N   PRO B 521 "
      ideal   model   delta    sigma   weight residual
     117.47  123.32   -5.85 1.16e+00 7.43e-01 2.55e+01
  angle pdb=" C   ILE L 106 "
        pdb=" N   LYS L 107 "
        pdb=" CA  LYS L 107 "
      ideal   model   delta    sigma   weight residual
     121.54  129.56   -8.02 1.91e+00 2.74e-01 1.76e+01
  angle pdb=" C   TYR A 204 "
        pdb=" N   SER A 205 "
        pdb=" CA  SER A 205 "
      ideal   model   delta    sigma   weight residual
     122.10  116.05    6.05 1.66e+00 3.63e-01 1.33e+01
  angle pdb=" N   GLN L 124 "
        pdb=" CA  GLN L 124 "
        pdb=" C   GLN L 124 "
      ideal   model   delta    sigma   weight residual
     111.07  107.30    3.77 1.07e+00 8.73e-01 1.24e+01
  angle pdb=" N   SER B 371 "
        pdb=" CA  SER B 371 "
        pdb=" C   SER B 371 "
      ideal   model   delta    sigma   weight residual
     114.56  110.16    4.40 1.27e+00 6.20e-01 1.20e+01
  ... (remaining 10030 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.86: 3946
       18.86 -    37.72: 405
       37.72 -    56.58: 61
       56.58 -    75.44: 25
       75.44 -    94.30: 8
  Dihedral angle restraints: 4445
    sinusoidal: 1815
      harmonic: 2630
  Sorted by residual:
  dihedral pdb=" CB  CYS A  15 "
           pdb=" SG  CYS A  15 "
           pdb=" SG  CYS A 136 "
           pdb=" CB  CYS A 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  149.28  -56.28     1      1.00e+01 1.00e-02 4.27e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.22   52.78     1      1.00e+01 1.00e-02 3.79e+01
  dihedral pdb=" CB  CYS H 160 "
           pdb=" SG  CYS H 160 "
           pdb=" SG  CYS H 216 "
           pdb=" CB  CYS H 216 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.52   52.48     1      1.00e+01 1.00e-02 3.75e+01
  ... (remaining 4442 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 981
       0.091 -    0.181: 121
       0.181 -    0.272: 11
       0.272 -    0.362: 1
       0.362 -    0.453: 2
  Chirality restraints: 1116
  Sorted by residual:
  chirality pdb=" C1  NAG A1301 "
            pdb=" ND2 ASN A  17 "
            pdb=" C2  NAG A1301 "
            pdb=" O5  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.95   -0.45 2.00e-01 2.50e+01 5.12e+00
  chirality pdb=" C1  NAG A1302 "
            pdb=" ND2 ASN A 165 "
            pdb=" C2  NAG A1302 "
            pdb=" O5  NAG A1302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.90e+00
  chirality pdb=" CB  VAL A 130 "
            pdb=" CA  VAL A 130 "
            pdb=" CG1 VAL A 130 "
            pdb=" CG2 VAL A 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 1113 not shown)

  Planarity restraints: 1290
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 138 "    0.048 5.00e-02 4.00e+02   7.23e-02 8.36e+00
        pdb=" N   PRO H 139 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO H 139 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO H 139 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 368 "    0.013 2.00e-02 2.50e+03   2.72e-02 7.38e+00
        pdb=" C   LEU B 368 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   LEU B 368 "    0.018 2.00e-02 2.50e+03
        pdb=" N   TYR B 369 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L 148 "    0.015 2.00e-02 2.50e+03   1.63e-02 6.64e+00
        pdb=" CG  TRP L 148 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP L 148 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP L 148 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP L 148 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP L 148 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP L 148 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L 148 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L 148 "    0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP L 148 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1287 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 553
        2.71 -     3.25: 7847
        3.25 -     3.80: 11838
        3.80 -     4.35: 14933
        4.35 -     4.90: 24653
  Nonbonded interactions: 59824
  Sorted by model distance:
  nonbonded pdb=" O   ASN H  53 "
            pdb=" OG  SER H  54 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" CG2 ILE L   2 "
            pdb=" N   GLN L   3 "
     model   vdw
     2.193 3.540
  nonbonded pdb=" N   GLY B 404 "
            pdb=" O   GLN B 506 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OD1 ASP A  53 "
            pdb=" N   LEU A  54 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" N   GLN H 191 "
            pdb=" O   LEU H 195 "
     model   vdw
     2.216 3.120
  ... (remaining 59819 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.160
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.093   7392  Z= 0.430
  Angle     :  1.095  12.851  10076  Z= 0.594
  Chirality :  0.062   0.453   1116
  Planarity :  0.006   0.072   1286
  Dihedral  : 15.983  94.299   2735
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 36.86
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 20.76 %
    Favored  : 78.91 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  1.40 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.80 (0.26), residues: 896
  helix: -3.80 (0.50), residues: 40
  sheet: -1.47 (0.32), residues: 269
  loop : -3.15 (0.24), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  19 
 TYR   0.034   0.003   TYR H  93 
 PHE   0.036   0.004   PHE B 377 
 TRP   0.042   0.004   TRP L 148 
 HIS   0.008   0.002   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00887 ( 7375)
  covalent geometry    : angle       1.05984 (10035)
  SS BOND              : bond        0.00803 (   10)
  SS BOND              : angle       2.67776 (   20)
  hydrogen bonds       : bond        0.13764 (  181)
  hydrogen bonds       : angle       9.33386 (  444)
  link_BETA1-4         : bond        0.00687 (    3)
  link_BETA1-4         : angle       4.96916 (    9)
  link_NAG-ASN         : bond        0.00939 (    4)
  link_NAG-ASN         : angle       6.06386 (   12)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 159
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 LYS cc_start: 0.7737 (ptmm) cc_final: 0.7101 (ptmm)
REVERT: A  224 GLU cc_start: 0.7897 (pm20) cc_final: 0.7502 (pm20)
REVERT: L  138 ASN cc_start: 0.8587 (m110) cc_final: 0.7973 (m110)
REVERT: L  192 TYR cc_start: 0.6668 (m-80) cc_final: 0.6386 (m-10)
  outliers start: 14
  outliers final: 5
  residues processed: 167
  average time/residue: 0.0856
  time to fit residues: 19.1105
Evaluate side-chains
  126 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 121
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 370 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 124 GLN
L 147 GLN
L 166 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.130484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.107627 restraints weight = 17942.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.110207 restraints weight = 10537.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.111975 restraints weight = 7221.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.113014 restraints weight = 5491.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.113894 restraints weight = 4571.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7392  Z= 0.177
  Angle     :  0.848  13.728  10076  Z= 0.423
  Chirality :  0.051   0.252   1116
  Planarity :  0.006   0.054   1286
  Dihedral  :  8.213  58.785   1130
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 18.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  7.99 %
    Favored  : 91.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.39 (0.27), residues: 896
  helix: -3.71 (0.48), residues: 39
  sheet: -1.33 (0.31), residues: 286
  loop : -2.79 (0.25), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  38 
 TYR   0.033   0.002   TYR L  91 
 PHE   0.013   0.002   PHE B 347 
 TRP   0.023   0.002   TRP L 148 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 7375)
  covalent geometry    : angle       0.81729 (10035)
  SS BOND              : bond        0.00394 (   10)
  SS BOND              : angle       1.43876 (   20)
  hydrogen bonds       : bond        0.04272 (  181)
  hydrogen bonds       : angle       7.97092 (  444)
  link_BETA1-4         : bond        0.00463 (    3)
  link_BETA1-4         : angle       3.80378 (    9)
  link_NAG-ASN         : bond        0.00637 (    4)
  link_NAG-ASN         : angle       5.55118 (   12)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 VAL cc_start: 0.7498 (p) cc_final: 0.6634 (p)
REVERT: A  191 GLU cc_start: 0.5896 (mm-30) cc_final: 0.5586 (mm-30)
REVERT: A  206 LYS cc_start: 0.7949 (ptmm) cc_final: 0.7476 (ptmm)
REVERT: A  224 GLU cc_start: 0.7786 (pm20) cc_final: 0.7434 (pm20)
REVERT: B  360 ASN cc_start: 0.8377 (t0) cc_final: 0.8167 (t0)
REVERT: B  466 ARG cc_start: 0.7650 (ttp80) cc_final: 0.6716 (ttt-90)
REVERT: B  516 GLU cc_start: 0.8273 (tp30) cc_final: 0.7985 (tm-30)
REVERT: H   31 ASP cc_start: 0.6905 (m-30) cc_final: 0.6539 (m-30)
REVERT: H   87 GLU cc_start: 0.8393 (pm20) cc_final: 0.8124 (pm20)
REVERT: L    4 MET cc_start: 0.6717 (tpt) cc_final: 0.6213 (tpt)
REVERT: L   21 ILE cc_start: 0.6931 (tp) cc_final: 0.6419 (mp)
REVERT: L  138 ASN cc_start: 0.8730 (m110) cc_final: 0.8246 (m110)
  outliers start: 1
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0818
  time to fit residues: 16.9131
Evaluate side-chains
  130 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 68 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 73 optimal weight:    8.9990
   chunk 27 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 76 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 59 optimal weight:    8.9990
   chunk 57 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  75 ASN
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 124 GLN
** L 147 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 = 0.3851 r_free = 0.3851 target = 0.128825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.106388 restraints weight = 17634.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.108909 restraints weight = 10359.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.110561 restraints weight = 7094.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.111607 restraints weight = 5437.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.112255 restraints weight = 4524.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   7392  Z= 0.248
  Angle     :  0.874  14.532  10076  Z= 0.438
  Chirality :  0.051   0.314   1116
  Planarity :  0.006   0.059   1286
  Dihedral  :  7.980  54.211   1130
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 20.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.96 %
    Favored  : 83.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.44 (0.27), residues: 896
  helix: -3.30 (0.60), residues: 39
  sheet: -1.55 (0.30), residues: 301
  loop : -2.77 (0.25), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  18 
 TYR   0.032   0.003   TYR L 192 
 PHE   0.027   0.002   PHE B 347 
 TRP   0.027   0.003   TRP H 174 
 HIS   0.004   0.001   HIS H 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 ( 7375)
  covalent geometry    : angle       0.84398 (10035)
  SS BOND              : bond        0.00650 (   10)
  SS BOND              : angle       1.46415 (   20)
  hydrogen bonds       : bond        0.04316 (  181)
  hydrogen bonds       : angle       7.92011 (  444)
  link_BETA1-4         : bond        0.00470 (    3)
  link_BETA1-4         : angle       3.29792 (    9)
  link_NAG-ASN         : bond        0.00757 (    4)
  link_NAG-ASN         : angle       5.89094 (   12)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 GLU cc_start: 0.5899 (mm-30) cc_final: 0.5661 (mm-30)
REVERT: A  206 LYS cc_start: 0.8074 (ptmm) cc_final: 0.7582 (ptmm)
REVERT: A  224 GLU cc_start: 0.7734 (pm20) cc_final: 0.7467 (pm20)
REVERT: B  466 ARG cc_start: 0.7686 (ttp80) cc_final: 0.6599 (ttt-90)
REVERT: B  516 GLU cc_start: 0.8187 (tp30) cc_final: 0.7894 (tm-30)
REVERT: H   31 ASP cc_start: 0.7011 (m-30) cc_final: 0.6623 (m-30)
REVERT: H   87 GLU cc_start: 0.8411 (pm20) cc_final: 0.8104 (pm20)
REVERT: L   18 ARG cc_start: 0.8459 (tpt90) cc_final: 0.8180 (tpt90)
REVERT: L   21 ILE cc_start: 0.6381 (tp) cc_final: 0.5861 (mp)
REVERT: L   91 TYR cc_start: 0.7283 (p90) cc_final: 0.6964 (p90)
REVERT: L  138 ASN cc_start: 0.8761 (m110) cc_final: 0.8040 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.0881
  time to fit residues: 17.7382
Evaluate side-chains
  122 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 79 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 ASN
** L 147 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 = 0.3913 r_free = 0.3913 target = 0.133696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.110481 restraints weight = 17643.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.113220 restraints weight = 10139.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.115040 restraints weight = 6844.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.116294 restraints weight = 5143.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.117033 restraints weight = 4204.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6922
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7392  Z= 0.151
  Angle     :  0.786  14.431  10076  Z= 0.393
  Chirality :  0.049   0.279   1116
  Planarity :  0.005   0.049   1286
  Dihedral  :  7.229  47.688   1130
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.83 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  5.33 %
    Favored  : 94.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.13 (0.28), residues: 896
  helix: -3.98 (0.62), residues: 27
  sheet: -1.27 (0.31), residues: 298
  loop : -2.56 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  18 
 TYR   0.016   0.002   TYR L 192 
 PHE   0.017   0.002   PHE B 347 
 TRP   0.010   0.001   TRP L  35 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7375)
  covalent geometry    : angle       0.75633 (10035)
  SS BOND              : bond        0.00544 (   10)
  SS BOND              : angle       1.18952 (   20)
  hydrogen bonds       : bond        0.03696 (  181)
  hydrogen bonds       : angle       7.44228 (  444)
  link_BETA1-4         : bond        0.00610 (    3)
  link_BETA1-4         : angle       3.18596 (    9)
  link_NAG-ASN         : bond        0.00685 (    4)
  link_NAG-ASN         : angle       5.49435 (   12)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 171
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 LYS cc_start: 0.8043 (ptmm) cc_final: 0.7818 (ptmm)
REVERT: B  405 ASP cc_start: 0.8013 (p0) cc_final: 0.7422 (p0)
REVERT: B  466 ARG cc_start: 0.7693 (ttp80) cc_final: 0.6620 (ttt180)
REVERT: B  516 GLU cc_start: 0.8064 (tp30) cc_final: 0.7805 (tm-30)
REVERT: H   19 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8099 (ttp80)
REVERT: H   31 ASP cc_start: 0.7012 (m-30) cc_final: 0.6487 (m-30)
REVERT: H   87 GLU cc_start: 0.8469 (pm20) cc_final: 0.8078 (pm20)
REVERT: H  181 SER cc_start: 0.7626 (t) cc_final: 0.7247 (m)
REVERT: L    4 MET cc_start: 0.6451 (tpt) cc_final: 0.6049 (tpt)
REVERT: L   82 ASP cc_start: 0.8387 (m-30) cc_final: 0.7101 (m-30)
REVERT: L  132 VAL cc_start: 0.8349 (t) cc_final: 0.8033 (m)
REVERT: L  138 ASN cc_start: 0.8648 (m110) cc_final: 0.8126 (m110)
  outliers start: 1
  outliers final: 0
  residues processed: 172
  average time/residue: 0.0825
  time to fit residues: 19.2143
Evaluate side-chains
  131 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 28 optimal weight:    0.4980
   chunk 16 optimal weight:    0.3980
   chunk 76 optimal weight:    0.9980
   chunk 75 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 37 optimal weight:    8.9990
   chunk 87 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 ASN
L 124 GLN
L 147 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.136308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.112911 restraints weight = 17236.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.115678 restraints weight = 9933.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.117556 restraints weight = 6723.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.118787 restraints weight = 5082.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.119531 restraints weight = 4151.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7392  Z= 0.135
  Angle     :  0.780  13.929  10076  Z= 0.385
  Chirality :  0.050   0.242   1116
  Planarity :  0.005   0.047   1286
  Dihedral  :  6.730  47.777   1130
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.50 %
    Favored  : 88.50 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.43 %
    Favored  : 96.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.03 (0.28), residues: 896
  helix: -3.81 (0.59), residues: 33
  sheet: -1.19 (0.30), residues: 298
  loop : -2.48 (0.26), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 403 
 TYR   0.015   0.002   TYR B 451 
 PHE   0.020   0.002   PHE H 166 
 TRP   0.032   0.002   TRP H 174 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7375)
  covalent geometry    : angle       0.75199 (10035)
  SS BOND              : bond        0.00337 (   10)
  SS BOND              : angle       1.28980 (   20)
  hydrogen bonds       : bond        0.03569 (  181)
  hydrogen bonds       : angle       7.20956 (  444)
  link_BETA1-4         : bond        0.00510 (    3)
  link_BETA1-4         : angle       3.04560 (    9)
  link_NAG-ASN         : bond        0.00673 (    4)
  link_NAG-ASN         : angle       5.29482 (   12)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 173
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8096 (ttp80)
REVERT: H   87 GLU cc_start: 0.8433 (pm20) cc_final: 0.8110 (pm20)
REVERT: H  181 SER cc_start: 0.7367 (t) cc_final: 0.7086 (m)
REVERT: H  224 ASN cc_start: 0.8136 (m-40) cc_final: 0.7322 (p0)
REVERT: L  132 VAL cc_start: 0.8364 (t) cc_final: 0.7807 (m)
REVERT: L  138 ASN cc_start: 0.8482 (m110) cc_final: 0.7911 (m110)
  outliers start: 1
  outliers final: 0
  residues processed: 174
  average time/residue: 0.0858
  time to fit residues: 20.0331
Evaluate side-chains
  132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 50 optimal weight:    8.9990
   chunk 51 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0770
   chunk 29 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 44 optimal weight:    7.9990
   chunk 3 optimal weight:    8.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.7742

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

Flipped N/Q/H residues before XYZ refinement:
A  69 HIS
A 146 HIS
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 ASN
H  82 ASN
** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 189 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.135622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.111996 restraints weight = 17272.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.114718 restraints weight = 10015.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.116574 restraints weight = 6781.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.117774 restraints weight = 5131.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.118601 restraints weight = 4218.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.3135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7392  Z= 0.152
  Angle     :  0.769  13.690  10076  Z= 0.382
  Chirality :  0.050   0.271   1116
  Planarity :  0.005   0.054   1286
  Dihedral  :  6.682  48.201   1130
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.50 %
    Favored  : 88.50 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.16 %
    Favored  : 97.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.28), residues: 896
  helix: -3.84 (0.59), residues: 33
  sheet: -0.97 (0.31), residues: 282
  loop : -2.40 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 403 
 TYR   0.023   0.002   TYR L 140 
 PHE   0.028   0.002   PHE A  58 
 TRP   0.011   0.001   TRP L  35 
 HIS   0.004   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7375)
  covalent geometry    : angle       0.73951 (10035)
  SS BOND              : bond        0.00528 (   10)
  SS BOND              : angle       1.69227 (   20)
  hydrogen bonds       : bond        0.03460 (  181)
  hydrogen bonds       : angle       7.08243 (  444)
  link_BETA1-4         : bond        0.00537 (    3)
  link_BETA1-4         : angle       2.98113 (    9)
  link_NAG-ASN         : bond        0.00610 (    4)
  link_NAG-ASN         : angle       5.29709 (   12)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  466 ARG cc_start: 0.7579 (ttp80) cc_final: 0.6824 (ptm160)
REVERT: H   19 ARG cc_start: 0.8246 (ttp80) cc_final: 0.8027 (ttp80)
REVERT: H   31 ASP cc_start: 0.6856 (m-30) cc_final: 0.6492 (m-30)
REVERT: H   87 GLU cc_start: 0.8370 (pm20) cc_final: 0.8070 (pm20)
REVERT: H  190 LEU cc_start: 0.8243 (tp) cc_final: 0.7615 (mp)
REVERT: H  224 ASN cc_start: 0.8038 (m-40) cc_final: 0.7260 (p0)
REVERT: L  132 VAL cc_start: 0.8247 (t) cc_final: 0.7946 (m)
REVERT: L  138 ASN cc_start: 0.8370 (m110) cc_final: 0.7615 (m110)
  outliers start: 1
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0875
  time to fit residues: 19.6643
Evaluate side-chains
  132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 63 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
A 148 ASN
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 ASN
** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 189 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.133123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.109434 restraints weight = 17473.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.112080 restraints weight = 10312.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.113805 restraints weight = 7064.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.114839 restraints weight = 5440.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.115624 restraints weight = 4562.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   7392  Z= 0.205
  Angle     :  0.812  13.984  10076  Z= 0.405
  Chirality :  0.050   0.307   1116
  Planarity :  0.006   0.053   1286
  Dihedral  :  6.987  47.678   1130
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 18.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.17 %
    Favored  : 85.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.87 (0.27), residues: 896
  helix: -3.84 (0.63), residues: 33
  sheet: -0.90 (0.32), residues: 272
  loop : -2.44 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  18 
 TYR   0.033   0.002   TYR B 365 
 PHE   0.027   0.002   PHE B 497 
 TRP   0.042   0.002   TRP H 174 
 HIS   0.006   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 7375)
  covalent geometry    : angle       0.78319 (10035)
  SS BOND              : bond        0.00565 (   10)
  SS BOND              : angle       1.70009 (   20)
  hydrogen bonds       : bond        0.03739 (  181)
  hydrogen bonds       : angle       7.18839 (  444)
  link_BETA1-4         : bond        0.00671 (    3)
  link_BETA1-4         : angle       2.90197 (    9)
  link_NAG-ASN         : bond        0.00687 (    4)
  link_NAG-ASN         : angle       5.48993 (   12)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 ARG cc_start: 0.8401 (ttp80) cc_final: 0.7855 (ttp80)
REVERT: H   31 ASP cc_start: 0.7058 (m-30) cc_final: 0.6664 (m-30)
REVERT: H   51 ILE cc_start: 0.9092 (tt) cc_final: 0.8892 (tt)
REVERT: H   87 GLU cc_start: 0.8501 (pm20) cc_final: 0.8146 (pm20)
REVERT: H  181 SER cc_start: 0.7585 (t) cc_final: 0.7231 (m)
REVERT: L  132 VAL cc_start: 0.8408 (t) cc_final: 0.8016 (m)
REVERT: L  138 ASN cc_start: 0.8636 (m110) cc_final: 0.7860 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.0815
  time to fit residues: 18.9511
Evaluate side-chains
  132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 78 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 9 optimal weight:    9.9990
   chunk 42 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0020
   overall best weight:    1.9794

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 189 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.135134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.111432 restraints weight = 17479.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.114112 restraints weight = 10057.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.115925 restraints weight = 6832.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.117017 restraints weight = 5190.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.117827 restraints weight = 4319.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7392  Z= 0.160
  Angle     :  0.792  13.955  10076  Z= 0.394
  Chirality :  0.050   0.294   1116
  Planarity :  0.005   0.052   1286
  Dihedral  :  6.815  48.551   1130
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 17.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.94 %
    Favored  : 88.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.78 (0.27), residues: 896
  helix: -3.27 (0.62), residues: 39
  sheet: -0.86 (0.32), residues: 279
  loop : -2.39 (0.25), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  18 
 TYR   0.021   0.002   TYR L 140 
 PHE   0.022   0.002   PHE B 347 
 TRP   0.015   0.002   TRP L  35 
 HIS   0.008   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7375)
  covalent geometry    : angle       0.76352 (10035)
  SS BOND              : bond        0.00353 (   10)
  SS BOND              : angle       1.50215 (   20)
  hydrogen bonds       : bond        0.03483 (  181)
  hydrogen bonds       : angle       7.12083 (  444)
  link_BETA1-4         : bond        0.00773 (    3)
  link_BETA1-4         : angle       2.91498 (    9)
  link_NAG-ASN         : bond        0.00697 (    4)
  link_NAG-ASN         : angle       5.36278 (   12)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.8711 (tptt) cc_final: 0.8509 (tptt)
REVERT: B  466 ARG cc_start: 0.7761 (ttp80) cc_final: 0.6807 (ptm160)
REVERT: B  516 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6790 (tm-30)
REVERT: H   31 ASP cc_start: 0.7055 (m-30) cc_final: 0.6646 (m-30)
REVERT: H   87 GLU cc_start: 0.8511 (pm20) cc_final: 0.8145 (pm20)
REVERT: H  224 ASN cc_start: 0.8275 (m-40) cc_final: 0.7463 (p0)
REVERT: L   21 ILE cc_start: 0.6270 (tp) cc_final: 0.6040 (tp)
REVERT: L  132 VAL cc_start: 0.8413 (t) cc_final: 0.8012 (m)
REVERT: L  138 ASN cc_start: 0.8608 (m110) cc_final: 0.7909 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.0844
  time to fit residues: 19.8894
Evaluate side-chains
  139 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 11 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 86 optimal weight:    5.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 189 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.132400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.108683 restraints weight = 17355.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.111320 restraints weight = 9992.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.113082 restraints weight = 6777.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.114289 restraints weight = 5177.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.114968 restraints weight = 4279.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.3135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7392  Z= 0.217
  Angle     :  0.846  13.633  10076  Z= 0.421
  Chirality :  0.051   0.300   1116
  Planarity :  0.006   0.060   1286
  Dihedral  :  7.124  47.443   1130
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 19.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.40 %
    Favored  : 84.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.85 (0.27), residues: 896
  helix: -3.76 (0.62), residues: 33
  sheet: -0.89 (0.32), residues: 279
  loop : -2.44 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H  19 
 TYR   0.028   0.003   TYR H  78 
 PHE   0.029   0.002   PHE B 497 
 TRP   0.052   0.003   TRP H 174 
 HIS   0.009   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 7375)
  covalent geometry    : angle       0.81701 (10035)
  SS BOND              : bond        0.00408 (   10)
  SS BOND              : angle       2.02718 (   20)
  hydrogen bonds       : bond        0.03908 (  181)
  hydrogen bonds       : angle       7.18598 (  444)
  link_BETA1-4         : bond        0.00516 (    3)
  link_BETA1-4         : angle       2.84995 (    9)
  link_NAG-ASN         : bond        0.00650 (    4)
  link_NAG-ASN         : angle       5.48567 (   12)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   31 ASP cc_start: 0.7105 (m-30) cc_final: 0.6768 (m-30)
REVERT: H   72 ASN cc_start: 0.7238 (m-40) cc_final: 0.7021 (m-40)
REVERT: H   87 GLU cc_start: 0.8478 (pm20) cc_final: 0.8122 (pm20)
REVERT: L   21 ILE cc_start: 0.6217 (tp) cc_final: 0.5953 (tp)
REVERT: L  132 VAL cc_start: 0.8291 (t) cc_final: 0.7930 (m)
REVERT: L  138 ASN cc_start: 0.8720 (m110) cc_final: 0.7950 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0814
  time to fit residues: 17.9021
Evaluate side-chains
  130 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 189 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.134337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.110323 restraints weight = 17470.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.113040 restraints weight = 10019.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.114769 restraints weight = 6784.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.116066 restraints weight = 5192.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.116787 restraints weight = 4264.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.3336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7392  Z= 0.175
  Angle     :  0.817  13.671  10076  Z= 0.407
  Chirality :  0.050   0.302   1116
  Planarity :  0.006   0.048   1286
  Dihedral  :  6.919  48.136   1130
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 17.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.28 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.77 (0.27), residues: 896
  helix: -3.77 (0.63), residues: 33
  sheet: -0.81 (0.32), residues: 279
  loop : -2.39 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 403 
 TYR   0.025   0.002   TYR L 140 
 PHE   0.035   0.002   PHE B 497 
 TRP   0.030   0.002   TRP L  35 
 HIS   0.008   0.002   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 7375)
  covalent geometry    : angle       0.78841 (10035)
  SS BOND              : bond        0.00344 (   10)
  SS BOND              : angle       1.88000 (   20)
  hydrogen bonds       : bond        0.03665 (  181)
  hydrogen bonds       : angle       7.07709 (  444)
  link_BETA1-4         : bond        0.00621 (    3)
  link_BETA1-4         : angle       2.83028 (    9)
  link_NAG-ASN         : bond        0.00702 (    4)
  link_NAG-ASN         : angle       5.33518 (   12)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  516 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6858 (tm-30)
REVERT: H   19 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8103 (ttp80)
REVERT: H   31 ASP cc_start: 0.7071 (m-30) cc_final: 0.6677 (m-30)
REVERT: H   87 GLU cc_start: 0.8485 (pm20) cc_final: 0.8128 (pm20)
REVERT: H  184 HIS cc_start: 0.7305 (m-70) cc_final: 0.6866 (m-70)
REVERT: H  186 PHE cc_start: 0.8029 (m-10) cc_final: 0.7806 (m-10)
REVERT: L    4 MET cc_start: 0.6436 (tpt) cc_final: 0.6097 (tpt)
REVERT: L   91 TYR cc_start: 0.7398 (p90) cc_final: 0.6953 (p90)
REVERT: L  132 VAL cc_start: 0.8260 (t) cc_final: 0.7902 (m)
REVERT: L  138 ASN cc_start: 0.8719 (m110) cc_final: 0.7906 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0765
  time to fit residues: 17.6625
Evaluate side-chains
  138 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 73 optimal weight:   20.0000
   chunk 47 optimal weight:    7.9990
   chunk 79 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0970
   chunk 25 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 52 optimal weight:    8.9990
   chunk 72 optimal weight:    0.5980
   chunk 62 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    2.7382

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 189 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.133843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.109986 restraints weight = 17393.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.112649 restraints weight = 10050.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.114447 restraints weight = 6823.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.115654 restraints weight = 5205.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.116348 restraints weight = 4289.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7392  Z= 0.186
  Angle     :  0.818  13.686  10076  Z= 0.406
  Chirality :  0.050   0.306   1116
  Planarity :  0.005   0.044   1286
  Dihedral  :  6.947  47.769   1130
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 17.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.81 (0.27), residues: 896
  helix: -3.72 (0.67), residues: 33
  sheet: -0.84 (0.32), residues: 279
  loop : -2.42 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 403 
 TYR   0.025   0.002   TYR L 140 
 PHE   0.037   0.002   PHE B 497 
 TRP   0.027   0.002   TRP L  35 
 HIS   0.012   0.002   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 7375)
  covalent geometry    : angle       0.79051 (10035)
  SS BOND              : bond        0.00351 (   10)
  SS BOND              : angle       1.56248 (   20)
  hydrogen bonds       : bond        0.03675 (  181)
  hydrogen bonds       : angle       7.10077 (  444)
  link_BETA1-4         : bond        0.00597 (    3)
  link_BETA1-4         : angle       2.82252 (    9)
  link_NAG-ASN         : bond        0.00690 (    4)
  link_NAG-ASN         : angle       5.39437 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1239.80 seconds
wall clock time: 22 minutes 10.96 seconds (1330.96 seconds total)