Starting phenix.real_space_refine
on Fri Aug 22 19:14:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bls_44675/08_2025/9bls_44675.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bls_44675/08_2025/9bls_44675.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bls_44675/08_2025/9bls_44675.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bls_44675/08_2025/9bls_44675.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bls_44675/08_2025/9bls_44675.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bls_44675/08_2025/9bls_44675.map"
  }
  resolution = 2.96
  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=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4471      2.51       5
     N    1229      2.21       5
     O    1385      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7112
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 594, 4516
          Classifications: {'peptide': 594}
          Link IDs: {'PTRANS': 21, 'TRANS': 572}
    Chain: "B"
      Number of atoms: 1277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1277
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 7, 'TRANS': 153}
    Chain: "C"
      Number of atoms: 1266
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 1266
          Classifications: {'peptide': 159}
          Link IDs: {'PTRANS': 7, 'TRANS': 151}
    Chain: "D"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 53
          Classifications: {'peptide': 7}
          Link IDs: {'TRANS': 6}
  Time building chain proxies: 1.82, per 1000 atoms: 0.26
  Number of scatterers: 7112
  At special positions: 0
  Unit cell: (73.865, 120.615, 118.745, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1385      8.00
     N    1229      7.00
     C    4471      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 342.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 12 sheets defined
      45.9% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 120 through 123
    Processing helix  chain 'A' and resid 130 through 140
      removed outlier: 4.106A  pdb=" N   LYS A 138 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ASN A 139 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 183
      removed outlier: 3.670A  pdb=" N   GLY A 167 " --> pdb=" O   PRO A 163 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TYR A 181 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 212
    Processing helix  chain 'A' and resid 222 through 231
    Processing helix  chain 'A' and resid 258 through 261
    Processing helix  chain 'A' and resid 274 through 294
      removed outlier: 4.224A  pdb=" N   PHE A 278 " --> pdb=" O   GLY A 274 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASP A 279 " --> pdb=" O   GLY A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 319
    Processing helix  chain 'A' and resid 348 through 355
    Processing helix  chain 'A' and resid 355 through 361
    Processing helix  chain 'A' and resid 363 through 373
    Processing helix  chain 'A' and resid 387 through 391
      removed outlier: 3.740A  pdb=" N   ARG A 391 " --> pdb=" O   GLY A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 404
    Processing helix  chain 'A' and resid 412 through 415
    Processing helix  chain 'A' and resid 416 through 429
    Processing helix  chain 'A' and resid 432 through 437
    Processing helix  chain 'A' and resid 556 through 561
    Processing helix  chain 'A' and resid 563 through 568
      removed outlier: 3.803A  pdb=" N   LYS A 567 " --> pdb=" O   LYS A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 597
    Processing helix  chain 'A' and resid 604 through 608
      removed outlier: 4.370A  pdb=" N   GLU A 607 " --> pdb=" O   PRO A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 619
      removed outlier: 4.035A  pdb=" N   GLU A 613 " --> pdb=" O   ASN A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 102
      removed outlier: 3.640A  pdb=" N   GLU B  97 " --> pdb=" O   GLN B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 125
      removed outlier: 4.775A  pdb=" N   GLU B 113 " --> pdb=" O   LYS B 109 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   VAL B 114 " --> pdb=" O   ASP B 110 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL B 125 " --> pdb=" O   ALA B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 158
    Processing helix  chain 'C' and resid 60 through 125
      removed outlier: 3.987A  pdb=" N   LYS C  64 " --> pdb=" O   LEU C  60 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL C  65 " --> pdb=" O   LEU C  61 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLU C  86 " --> pdb=" O   LEU C  82 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ASP C 110 " --> pdb=" O   ALA C 106 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   GLU C 113 " --> pdb=" O   LYS C 109 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   VAL C 114 " --> pdb=" O   ASP C 110 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA C 115 " --> pdb=" O   LEU C 111 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL C 125 " --> pdb=" O   ALA C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 130
      removed outlier: 3.787A  pdb=" N   ILE C 130 " --> pdb=" O   LYS C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 134 through 158
    Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 77
      removed outlier: 3.946A  pdb=" N   GLN A  74 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 77
      removed outlier: 3.946A  pdb=" N   GLN A  74 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   MET A  70 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   VAL A  55 " --> pdb=" O   MET A  70 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   VAL A  56 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   THR A 192 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   ILE A  58 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ALA A 189 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   ARG A 218 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 101
    Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 146
      removed outlier: 4.494A  pdb=" N   LYS A 143 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 270
      removed outlier: 5.580A  pdb=" N   VAL A 264 " --> pdb=" O   GLU A 256 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   GLU A 256 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLU A 382 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 335
      removed outlier: 3.849A  pdb=" N   TYR A 331 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   LYS A 340 " --> pdb=" O   TYR A 331 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   THR A 333 " --> pdb=" O   GLY A 338 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   GLY A 338 " --> pdb=" O   THR A 333 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 455 through 458
      removed outlier: 5.517A  pdb=" N   LYS A 456 " --> pdb=" O   ILE A 447 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   ILE A 447 " --> pdb=" O   LYS A 456 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLY A 501 " --> pdb=" O   VAL A 486 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 466 through 473
      removed outlier: 3.578A  pdb=" N   ILE A 524 " --> pdb=" O   THR A 466 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 160 through 163
      removed outlier: 6.526A  pdb=" N   TYR B 199 " --> pdb=" O   LEU B 206 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 175 through 179
      removed outlier: 7.250A  pdb=" N   VAL B 213 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   LEU B 210 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   VAL B 194 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   GLY B 212 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 160 through 163
      removed outlier: 6.378A  pdb=" N   TYR C 199 " --> pdb=" O   LEU C 206 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 175 through 180
      removed outlier: 7.524A  pdb=" N   VAL C 213 " --> pdb=" O   LEU C 178 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   HIS C 180 " --> pdb=" O   VAL C 213 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   LEU C 210 " --> pdb=" O   VAL C 194 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   VAL C 194 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   GLY C 212 " --> pdb=" O   ALA C 192 " (cutoff:3.500A)

    386 hydrogen bonds defined for protein.
    1113 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: 0.82

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2408
        1.34 -     1.46: 1349
        1.46 -     1.58: 3405
        1.58 -     1.70: 0
        1.70 -     1.82: 45
  Bond restraints: 7207
  Sorted by residual:
  bond pdb=" CB  GLU B  97 "
       pdb=" CG  GLU B  97 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.03e+00
  bond pdb=" SD  MET A 174 "
       pdb=" CE  MET A 174 "
    ideal  model  delta    sigma   weight residual
    1.791  1.766  0.025 2.50e-02 1.60e+03 9.80e-01
  bond pdb=" CB  GLU A 374 "
       pdb=" CG  GLU A 374 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.46e-01
  bond pdb=" CB  GLU C 148 "
       pdb=" CG  GLU C 148 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.43e-01
  bond pdb=" CG  GLU B  97 "
       pdb=" CD  GLU B  97 "
    ideal  model  delta    sigma   weight residual
    1.516  1.534 -0.018 2.50e-02 1.60e+03 5.39e-01
  ... (remaining 7202 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 9652
        2.45 -     4.89: 60
        4.89 -     7.34: 8
        7.34 -     9.78: 1
        9.78 -    12.23: 1
  Bond angle restraints: 9722
  Sorted by residual:
  angle pdb=" CB  MET A 618 "
        pdb=" CG  MET A 618 "
        pdb=" SD  MET A 618 "
      ideal   model   delta    sigma   weight residual
     112.70  124.93  -12.23 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" CA  GLN A 108 "
        pdb=" CB  GLN A 108 "
        pdb=" CG  GLN A 108 "
      ideal   model   delta    sigma   weight residual
     114.10  119.09   -4.99 2.00e+00 2.50e-01 6.24e+00
  angle pdb=" CB  GLU B  97 "
        pdb=" CG  GLU B  97 "
        pdb=" CD  GLU B  97 "
      ideal   model   delta    sigma   weight residual
     112.60  116.77   -4.17 1.70e+00 3.46e-01 6.03e+00
  angle pdb=" CB  GLU A 374 "
        pdb=" CG  GLU A 374 "
        pdb=" CD  GLU A 374 "
      ideal   model   delta    sigma   weight residual
     112.60  116.40   -3.80 1.70e+00 3.46e-01 5.00e+00
  angle pdb=" CG  MET A 618 "
        pdb=" SD  MET A 618 "
        pdb=" CE  MET A 618 "
      ideal   model   delta    sigma   weight residual
     100.90  105.78   -4.88 2.20e+00 2.07e-01 4.92e+00
  ... (remaining 9717 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 3654
       17.10 -    34.20: 550
       34.20 -    51.30: 196
       51.30 -    68.40: 55
       68.40 -    85.50: 12
  Dihedral angle restraints: 4467
    sinusoidal: 1823
      harmonic: 2644
  Sorted by residual:
  dihedral pdb=" CA  GLY B 103 "
           pdb=" C   GLY B 103 "
           pdb=" N   ILE B 104 "
           pdb=" CA  ILE B 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.63   17.37     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  GLY A 528 "
           pdb=" C   GLY A 528 "
           pdb=" N   ILE A 529 "
           pdb=" CA  ILE A 529 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.97  -17.03     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CG  ARG A 309 "
           pdb=" CD  ARG A 309 "
           pdb=" NE  ARG A 309 "
           pdb=" CZ  ARG A 309 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.24  -43.76     2      1.50e+01 4.44e-03 1.02e+01
  ... (remaining 4464 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 733
       0.031 -    0.063: 274
       0.063 -    0.094: 77
       0.094 -    0.126: 45
       0.126 -    0.157: 3
  Chirality restraints: 1132
  Sorted by residual:
  chirality pdb=" CB  ILE A 257 "
            pdb=" CA  ILE A 257 "
            pdb=" CG1 ILE A 257 "
            pdb=" CG2 ILE A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.16 2.00e-01 2.50e+01 6.15e-01
  chirality pdb=" CA  VAL A 193 "
            pdb=" N   VAL A 193 "
            pdb=" C   VAL A 193 "
            pdb=" CB  VAL A 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.97e-01
  chirality pdb=" CA  VAL B 125 "
            pdb=" N   VAL B 125 "
            pdb=" C   VAL B 125 "
            pdb=" CB  VAL B 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.95e-01
  ... (remaining 1129 not shown)

  Planarity restraints: 1265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 103 "    0.036 5.00e-02 4.00e+02   5.49e-02 4.83e+00
        pdb=" N   PRO A 104 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 104 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 104 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 374 "    0.007 2.00e-02 2.50e+03   1.53e-02 2.33e+00
        pdb=" CD  GLU A 374 "   -0.026 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 374 "    0.010 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 374 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 120 "    0.007 2.00e-02 2.50e+03   1.39e-02 1.93e+00
        pdb=" C   THR A 120 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   THR A 120 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LYS A 121 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1262 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1084
        2.76 -     3.29: 6665
        3.29 -     3.83: 11707
        3.83 -     4.36: 13334
        4.36 -     4.90: 24319
  Nonbonded interactions: 57109
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 474 "
            pdb=" OE1 GLN A 479 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OG1 THR A 441 "
            pdb=" O   ARG A 460 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" NH1 ARG A 578 "
            pdb=" OH  TYR C 173 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" OD2 ASP B 116 "
            pdb=" NH1 ARG B 207 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" O   GLU A 352 "
            pdb=" OG1 THR A 356 "
     model   vdw
     2.278 3.040
  ... (remaining 57104 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 59 through 217)
  selection = chain 'C'
}

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 individual isotropic
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:             4.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.220
  Find NCS groups from input model:        0.060
  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:7.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
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      :  0.003   0.035   7207  Z= 0.134
  Angle     :  0.510  12.229   9722  Z= 0.254
  Chirality :  0.040   0.157   1132
  Planarity :  0.003   0.055   1265
  Dihedral  : 19.379  85.504   2759
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 36.18 %
    Favored  : 60.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.28), residues: 913
  helix:  1.53 (0.26), residues: 389
  sheet: -0.05 (0.49), residues: 125
  loop : -1.11 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 578 
 TYR   0.014   0.001   TYR B 102 
 PHE   0.008   0.001   PHE A 142 
 TRP   0.001   0.000   TRP A 126 
 HIS   0.003   0.001   HIS B 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7207)
  covalent geometry    : angle       0.51018 ( 9722)
  hydrogen bonds       : bond        0.15852 (  383)
  hydrogen bonds       : angle       6.24754 ( 1113)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6783 (tm-30)
REVERT: A  258 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6529 (pm20)
REVERT: A  498 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6474 (mptt)
REVERT: A  547 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6908 (tp)
REVERT: B   93 GLN cc_start: 0.7350 (mt0) cc_final: 0.7034 (mp10)
REVERT: B  201 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7974 (pt)
REVERT: D  438 LEU cc_start: 0.7903 (mt) cc_final: 0.7339 (mp)
  outliers start: 28
  outliers final: 20
  residues processed: 91
  average time/residue: 0.4440
  time to fit residues: 42.9946
Evaluate side-chains
  93 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  198 ASN
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  258 GLN
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  493 MET
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  606 ASP
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  625 LYS
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  197 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
B  90 GLN
B 123 GLN
C 136 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.176531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.128742 restraints weight = 7280.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.80
r_work: 0.3142 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.0893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.070   7207  Z= 0.299
  Angle     :  0.650   9.485   9722  Z= 0.338
  Chirality :  0.047   0.140   1132
  Planarity :  0.005   0.058   1265
  Dihedral  :  8.838  65.530   1025
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  8.79 %
    Allowed  : 30.49 %
    Favored  : 60.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.27), residues: 913
  helix:  1.16 (0.25), residues: 397
  sheet: -0.49 (0.45), residues: 134
  loop : -1.24 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 578 
 TYR   0.018   0.002   TYR B 102 
 PHE   0.013   0.002   PHE A 503 
 TRP   0.004   0.001   TRP A 126 
 HIS   0.006   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00742 ( 7207)
  covalent geometry    : angle       0.65029 ( 9722)
  hydrogen bonds       : bond        0.06039 (  383)
  hydrogen bonds       : angle       5.06447 ( 1113)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 75
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6887 (tm-30)
REVERT: A  316 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8191 (ttpp)
REVERT: A  340 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7470 (mmmt)
REVERT: A  405 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7368 (ttm-80)
REVERT: A  498 LYS cc_start: 0.7304 (mttt) cc_final: 0.6584 (mptt)
REVERT: A  523 ASP cc_start: 0.7515 (t70) cc_final: 0.7203 (m-30)
REVERT: B  148 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7141 (tt0)
REVERT: D  438 LEU cc_start: 0.7752 (mt) cc_final: 0.7219 (mp)
REVERT: D  439 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7844 (t0)
  outliers start: 68
  outliers final: 28
  residues processed: 128
  average time/residue: 0.5226
  time to fit residues: 70.8709
Evaluate side-chains
  105 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 71
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  198 ASN
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  316 LYS
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  405 ARG
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  197 VAL
Chi-restraints excluded: chain D residue  439 ASP
Chi-restraints excluded: chain D residue  441 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 46 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0980
   chunk 89 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 81 optimal weight:    0.3980
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 198 ASN
B  90 GLN
B 123 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.180988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.131471 restraints weight = 7199.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 1.80
r_work: 0.3216 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.0891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7207  Z= 0.131
  Angle     :  0.504   7.875   9722  Z= 0.262
  Chirality :  0.041   0.132   1132
  Planarity :  0.003   0.053   1265
  Dihedral  :  7.203  60.575    998
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  7.24 %
    Allowed  : 30.88 %
    Favored  : 61.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.28), residues: 913
  helix:  1.68 (0.26), residues: 391
  sheet: -0.29 (0.45), residues: 126
  loop : -1.14 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 578 
 TYR   0.013   0.001   TYR A 243 
 PHE   0.011   0.001   PHE A 503 
 TRP   0.003   0.001   TRP A 126 
 HIS   0.003   0.001   HIS B 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7207)
  covalent geometry    : angle       0.50356 ( 9722)
  hydrogen bonds       : bond        0.04419 (  383)
  hydrogen bonds       : angle       4.60622 ( 1113)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 75
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6733 (tm-30)
REVERT: A  198 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8353 (p0)
REVERT: A  340 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7369 (mmmt)
REVERT: A  405 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7338 (ttm-80)
REVERT: A  498 LYS cc_start: 0.7324 (mttt) cc_final: 0.6732 (mptt)
REVERT: A  523 ASP cc_start: 0.7437 (t70) cc_final: 0.7091 (m-30)
REVERT: A  613 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6265 (tp30)
REVERT: B   93 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.7020 (mt0)
REVERT: B  148 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7082 (tt0)
REVERT: B  187 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6611 (tm-30)
REVERT: C  113 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7079 (tp30)
REVERT: C  131 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7688 (pttp)
REVERT: D  438 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7079 (mp)
  outliers start: 56
  outliers final: 21
  residues processed: 120
  average time/residue: 0.4962
  time to fit residues: 63.2575
Evaluate side-chains
  101 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 70
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  198 ASN
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  405 ARG
Chi-restraints excluded: chain A residue  456 LYS
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  197 VAL
Chi-restraints excluded: chain D residue  438 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 86 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  90 GLN
B 123 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.179589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.128467 restraints weight = 7249.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.55
r_work: 0.3223 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.0974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7207  Z= 0.176
  Angle     :  0.543   8.149   9722  Z= 0.280
  Chirality :  0.043   0.139   1132
  Planarity :  0.004   0.054   1265
  Dihedral  :  7.113  62.357    996
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  8.14 %
    Allowed  : 30.36 %
    Favored  : 61.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.28), residues: 913
  helix:  1.63 (0.26), residues: 391
  sheet: -0.25 (0.45), residues: 126
  loop : -1.12 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 578 
 TYR   0.015   0.002   TYR A 243 
 PHE   0.011   0.001   PHE A 503 
 TRP   0.003   0.001   TRP A 126 
 HIS   0.004   0.001   HIS B 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 7207)
  covalent geometry    : angle       0.54333 ( 9722)
  hydrogen bonds       : bond        0.04759 (  383)
  hydrogen bonds       : angle       4.61357 ( 1113)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 76
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6696 (tm-30)
REVERT: A  340 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7358 (mmmt)
REVERT: A  405 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7292 (ttm-80)
REVERT: A  498 LYS cc_start: 0.7291 (mttt) cc_final: 0.6650 (mptt)
REVERT: A  523 ASP cc_start: 0.7428 (t70) cc_final: 0.7085 (m-30)
REVERT: A  547 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7011 (tp)
REVERT: A  613 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6262 (tp30)
REVERT: B   93 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6974 (mt0)
REVERT: B  148 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6987 (tt0)
REVERT: B  187 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6491 (tm-30)
REVERT: C  113 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6954 (tp30)
REVERT: C  131 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7643 (pttp)
REVERT: D  438 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.6938 (mp)
  outliers start: 63
  outliers final: 30
  residues processed: 126
  average time/residue: 0.5045
  time to fit residues: 67.3684
Evaluate side-chains
  111 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 71
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  198 ASN
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  405 ARG
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain C residue   90 GLN
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  197 VAL
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  441 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 68 optimal weight:    0.3980
   chunk 63 optimal weight:    0.0970
   chunk 64 optimal weight:    0.5980
   chunk 74 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0040
   overall best weight:    0.3390

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 123 GLN
B 150 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.182569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.133028 restraints weight = 7210.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.79
r_work: 0.3245 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.1069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7207  Z= 0.111
  Angle     :  0.490   9.242   9722  Z= 0.252
  Chirality :  0.040   0.131   1132
  Planarity :  0.003   0.051   1265
  Dihedral  :  6.689  59.717    996
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  6.98 %
    Allowed  : 32.17 %
    Favored  : 60.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.28), residues: 913
  helix:  1.91 (0.26), residues: 393
  sheet: -0.21 (0.45), residues: 126
  loop : -1.03 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 578 
 TYR   0.013   0.001   TYR A 243 
 PHE   0.009   0.001   PHE A 503 
 TRP   0.004   0.001   TRP A 126 
 HIS   0.003   0.001   HIS B 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 7207)
  covalent geometry    : angle       0.49038 ( 9722)
  hydrogen bonds       : bond        0.03989 (  383)
  hydrogen bonds       : angle       4.40784 ( 1113)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 74
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6683 (tm-30)
REVERT: A  198 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8382 (p0)
REVERT: A  498 LYS cc_start: 0.7321 (mttt) cc_final: 0.6753 (mptt)
REVERT: A  547 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.6924 (tp)
REVERT: A  613 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6287 (tp30)
REVERT: B   93 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6863 (mp10)
REVERT: B  148 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7088 (tt0)
REVERT: B  187 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6612 (tm-30)
REVERT: C  131 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7741 (pttp)
REVERT: D  438 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7149 (mp)
  outliers start: 54
  outliers final: 26
  residues processed: 118
  average time/residue: 0.4424
  time to fit residues: 55.5457
Evaluate side-chains
  105 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 71
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  198 ASN
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   90 GLN
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain D residue  438 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 123 GLN
C 139 ASN

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 = 0.177588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.119271 restraints weight = 7302.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 1.75
r_work: 0.3164 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.1114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   7207  Z= 0.258
  Angle     :  0.617   9.989   9722  Z= 0.314
  Chirality :  0.046   0.137   1132
  Planarity :  0.004   0.054   1265
  Dihedral  :  6.815  64.621    993
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  7.11 %
    Allowed  : 32.04 %
    Favored  : 60.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.28), residues: 913
  helix:  1.42 (0.25), residues: 397
  sheet: -0.08 (0.45), residues: 129
  loop : -1.19 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 578 
 TYR   0.017   0.002   TYR B 102 
 PHE   0.011   0.002   PHE A 503 
 TRP   0.004   0.001   TRP A 126 
 HIS   0.005   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00641 ( 7207)
  covalent geometry    : angle       0.61679 ( 9722)
  hydrogen bonds       : bond        0.05405 (  383)
  hydrogen bonds       : angle       4.71783 ( 1113)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 71
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A   74 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7655 (pt0)
REVERT: A  155 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6786 (tm-30)
REVERT: A  340 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7303 (mmmt)
REVERT: A  498 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6667 (mptt)
REVERT: A  523 ASP cc_start: 0.7471 (t70) cc_final: 0.7157 (m-30)
REVERT: A  547 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7036 (tp)
REVERT: B  148 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7061 (tt0)
REVERT: B  187 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6422 (tm-30)
REVERT: C  131 LYS cc_start: 0.7916 (mtmm) cc_final: 0.7609 (pttp)
REVERT: D  438 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7036 (mp)
  outliers start: 55
  outliers final: 32
  residues processed: 115
  average time/residue: 0.4737
  time to fit residues: 57.6901
Evaluate side-chains
  109 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 69
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue   74 GLN
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  198 ASN
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  326 ASP
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  519 GLU
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  441 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0870
   chunk 55 optimal weight:    6.9990
   chunk 69 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0980
   chunk 20 optimal weight:    0.5980
   chunk 57 optimal weight:    8.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 123 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.181127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.131981 restraints weight = 7257.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 2.07
r_work: 0.3202 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.1124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7207  Z= 0.128
  Angle     :  0.516  10.648   9722  Z= 0.263
  Chirality :  0.041   0.134   1132
  Planarity :  0.003   0.052   1265
  Dihedral  :  6.497  60.997    993
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 33.07 %
    Favored  : 60.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.28), residues: 913
  helix:  1.78 (0.26), residues: 391
  sheet: -0.18 (0.45), residues: 126
  loop : -1.09 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 578 
 TYR   0.015   0.001   TYR A 243 
 PHE   0.010   0.001   PHE A 503 
 TRP   0.005   0.001   TRP A 126 
 HIS   0.004   0.001   HIS B 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7207)
  covalent geometry    : angle       0.51636 ( 9722)
  hydrogen bonds       : bond        0.04262 (  383)
  hydrogen bonds       : angle       4.45975 ( 1113)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 73
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6796 (tm-30)
REVERT: A  303 MET cc_start: 0.8344 (mpm) cc_final: 0.8139 (mmt)
REVERT: A  340 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7440 (mmmt)
REVERT: A  498 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6674 (mptt)
REVERT: A  547 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7002 (tp)
REVERT: A  613 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6273 (tp30)
REVERT: B   93 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6995 (mp10)
REVERT: B  148 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7156 (tt0)
REVERT: B  187 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6565 (tm-30)
REVERT: C  113 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7166 (tp30)
REVERT: C  131 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7697 (pttp)
  outliers start: 47
  outliers final: 24
  residues processed: 110
  average time/residue: 0.4673
  time to fit residues: 54.5353
Evaluate side-chains
  104 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 71
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  198 ASN
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  193 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 36 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   chunk 88 optimal weight:    2.9990
   chunk 82 optimal weight:    0.2980
   chunk 33 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    0.3980
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 123 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.181024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.131662 restraints weight = 7259.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.07
r_work: 0.3145 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.1156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7207  Z= 0.139
  Angle     :  0.526  11.312   9722  Z= 0.267
  Chirality :  0.041   0.135   1132
  Planarity :  0.003   0.052   1265
  Dihedral  :  6.475  60.816    993
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 33.20 %
    Favored  : 60.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.28), residues: 913
  helix:  1.80 (0.26), residues: 392
  sheet: -0.25 (0.44), residues: 134
  loop : -1.05 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 578 
 TYR   0.015   0.001   TYR A 243 
 PHE   0.010   0.001   PHE A 503 
 TRP   0.004   0.001   TRP A 126 
 HIS   0.003   0.001   HIS B 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 7207)
  covalent geometry    : angle       0.52563 ( 9722)
  hydrogen bonds       : bond        0.04319 (  383)
  hydrogen bonds       : angle       4.41793 ( 1113)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 72
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6876 (tm-30)
REVERT: A  303 MET cc_start: 0.8365 (mpm) cc_final: 0.8161 (mmt)
REVERT: A  340 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7504 (mmmt)
REVERT: A  498 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6653 (mptt)
REVERT: A  519 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5719 (tt0)
REVERT: A  547 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.6961 (tp)
REVERT: A  613 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6262 (tp30)
REVERT: B   93 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7023 (mp10)
REVERT: B  148 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7274 (tt0)
REVERT: B  187 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6579 (tm-30)
REVERT: C  113 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7248 (tp30)
REVERT: C  131 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7731 (pttp)
  outliers start: 46
  outliers final: 26
  residues processed: 109
  average time/residue: 0.5018
  time to fit residues: 57.8641
Evaluate side-chains
  108 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 72
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  198 ASN
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  519 GLU
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  193 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 58 optimal weight:    0.1980
   chunk 67 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 123 GLN
C 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.181092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.130808 restraints weight = 7210.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.85
r_work: 0.3166 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7207  Z= 0.147
  Angle     :  0.534  10.987   9722  Z= 0.271
  Chirality :  0.041   0.135   1132
  Planarity :  0.003   0.051   1265
  Dihedral  :  6.490  60.690    993
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 33.33 %
    Favored  : 60.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.28), residues: 913
  helix:  1.83 (0.26), residues: 386
  sheet: -0.24 (0.45), residues: 134
  loop : -1.07 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 578 
 TYR   0.016   0.001   TYR A 128 
 PHE   0.010   0.001   PHE A 503 
 TRP   0.004   0.001   TRP A 126 
 HIS   0.003   0.001   HIS B 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 7207)
  covalent geometry    : angle       0.53361 ( 9722)
  hydrogen bonds       : bond        0.04372 (  383)
  hydrogen bonds       : angle       4.40599 ( 1113)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 71
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A  155 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6814 (tm-30)
REVERT: A  303 MET cc_start: 0.8348 (mpm) cc_final: 0.8138 (mmt)
REVERT: A  340 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7475 (mmmt)
REVERT: A  498 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6689 (mptt)
REVERT: A  502 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8149 (tt0)
REVERT: A  519 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5733 (tt0)
REVERT: A  547 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.6942 (tp)
REVERT: A  613 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6253 (tp30)
REVERT: B   93 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.7014 (mp10)
REVERT: B  148 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7200 (tt0)
REVERT: B  187 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6573 (tm-30)
REVERT: C  113 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7204 (tp30)
REVERT: C  131 LYS cc_start: 0.8018 (mtmm) cc_final: 0.7766 (pttp)
  outliers start: 44
  outliers final: 29
  residues processed: 106
  average time/residue: 0.4326
  time to fit residues: 48.5884
Evaluate side-chains
  110 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 70
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  198 ASN
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  488 GLN
Chi-restraints excluded: chain A residue  498 LYS
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  502 GLN
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  519 GLU
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain C residue   75 VAL
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue   90 GLN
Chi-restraints excluded: chain C residue  113 GLU
Chi-restraints excluded: chain C residue  193 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 51.2686 > 50:
  distance: 32 - 61:   5.863
  distance: 54 - 61:   3.813
  distance: 62 - 65:   3.302
  distance: 63 - 64:   7.382
  distance: 63 - 71:   8.029
  distance: 65 - 66:   5.778
  distance: 66 - 67:   5.479
  distance: 66 - 68:   8.656
  distance: 67 - 69:   6.312
  distance: 68 - 70:   9.448
  distance: 71 - 72:   4.910
  distance: 72 - 73:   4.567
  distance: 73 - 74:   6.456
  distance: 73 - 75:   4.874
  distance: 75 - 76:   3.117
  distance: 76 - 77:   6.901
  distance: 76 - 79:   4.300
  distance: 77 - 78:   5.641
  distance: 80 - 81:   7.163
  distance: 80 - 82:   8.285
  distance: 83 - 84:   5.825
  distance: 83 - 190:   6.267
  distance: 84 - 87:   4.574
  distance: 85 - 86:   6.602
  distance: 85 - 91:   4.985
  distance: 86 - 187:  13.204
  distance: 87 - 88:   5.591
  distance: 88 - 89:   6.511
  distance: 88 - 90:   9.666
  distance: 91 - 92:   3.947
  distance: 92 - 93:   3.128
  distance: 93 - 94:   7.086
  distance: 93 - 100:   6.441
  distance: 95 - 96:   5.246
  distance: 98 - 99:   4.686
  distance: 100 - 101:   7.752
  distance: 100 - 175:   4.465
  distance: 101 - 102:   5.596
  distance: 101 - 104:   7.221
  distance: 102 - 103:  25.958
  distance: 102 - 108:  25.348
  distance: 103 - 172:  33.991
  distance: 105 - 106:   8.955
  distance: 105 - 107:   5.747
  distance: 108 - 109:  31.749
  distance: 109 - 110:  12.183
  distance: 109 - 112:   5.501
  distance: 110 - 111:   9.479
  distance: 110 - 116:  13.901
  distance: 112 - 113:  18.321
  distance: 113 - 114:   4.310
  distance: 113 - 115:   7.795
  distance: 116 - 117:   5.900
  distance: 117 - 118:   5.002
  distance: 117 - 120:   5.653
  distance: 118 - 119:   3.370
  distance: 118 - 123:   6.692
  distance: 120 - 121:   7.828
  distance: 121 - 122:   6.110
  distance: 123 - 124:   6.217
  distance: 124 - 125:   4.015
  distance: 124 - 127:   7.870
  distance: 125 - 126:   7.130
  distance: 125 - 130:   7.677
  distance: 127 - 128:   5.713
  distance: 130 - 131:   5.764
  distance: 131 - 132:   6.021
  distance: 132 - 133:   5.547