Starting phenix.real_space_refine
on Tue May 13 07:23:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dao_46695/05_2025/9dao_46695_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dao_46695/05_2025/9dao_46695.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dao_46695/05_2025/9dao_46695.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dao_46695/05_2025/9dao_46695.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dao_46695/05_2025/9dao_46695_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dao_46695/05_2025/9dao_46695_neut.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.086
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: 6
    Type Number    sf(0)   Gaussians
     Ca      5      9.91       5
     Mg      1      5.21       5
     S      43      5.16       5
     C    6171      2.51       5
     N    1671      2.21       5
     O    1913      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9804
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3480
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 451, 3460
          Classifications: {'peptide': 451}
          Link IDs: {'PTRANS': 26, 'TRANS': 424}
      Conformer: "B"
        Number of residues, atoms: 451, 3460
          Classifications: {'peptide': 451}
          Link IDs: {'PTRANS': 26, 'TRANS': 424}
          bond proxies already assigned to first conformer: 3533
    Chain: "B"
      Number of atoms: 2914
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 372, 2910
          Classifications: {'peptide': 372}
          Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 353}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 372, 2910
          Classifications: {'peptide': 372}
          Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 353}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2957
    Chain: "H"
      Number of atoms: 1738
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 227, 1721
          Classifications: {'peptide': 227}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 212}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
      Conformer: "B"
        Number of residues, atoms: 227, 1721
          Classifications: {'peptide': 227}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 212}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          bond proxies already assigned to first conformer: 1747
    Chain: "L"
      Number of atoms: 1666
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 214, 1666
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 204}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' CA': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 1, ' MG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AGLN A 177 " occ=0.56
      ... (16 atoms not shown)
      pdb=" NE2BGLN A 177 " occ=0.44
    residue:
      pdb=" N  AARG A 276 " occ=0.43
      ... (20 atoms not shown)
      pdb=" NH2BARG A 276 " occ=0.57
    residue:
      pdb=" N  AARG H  98 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG H  98 " occ=0.50
    residue:
      pdb=" N   CYS L 214 " occ=0.15
      ... (5 atoms not shown)
      pdb=" OXT CYS L 214 " occ=0.15
  Time building chain proxies: 10.94, per 1000 atoms: 1.12
  Number of scatterers: 9804
  At special positions: 0
  Unit cell: (77.4, 123.84, 152.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      5     19.99
     S      43     16.00
     Mg      1     11.99
     O    1913      8.00
     N    1671      7.00
     C    6171      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  56 " - pdb=" SG  CYS A  65 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 130 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 146 " - pdb=" SG  CYS A 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 177 " - pdb=" SG  CYS B 184 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 374 " - pdb=" SG  CYS B 386 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 152 " - pdb=" SG  CYS H 207 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG ACYS L 194 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.38
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2326

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 23 sheets defined
      11.3% alpha, 34.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 151 through 158
      removed outlier: 3.600A  pdb=" N   TYR A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 200 through 206
    Processing helix  chain 'A' and resid 227 through 231
    Processing helix  chain 'A' and resid 259 through 264
    Processing helix  chain 'B' and resid 127 through 134
    Processing helix  chain 'B' and resid 137 through 146
      removed outlier: 3.923A  pdb=" N   MET B 142 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ARG B 143 " --> pdb=" O   ALA B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 209
      removed outlier: 3.701A  pdb=" N   PHE B 203 " --> pdb=" O   GLN B 199 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LYS B 209 " --> pdb=" O   GLU B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 232
    Processing helix  chain 'B' and resid 232 through 237
    Processing helix  chain 'B' and resid 258 through 264
      removed outlier: 3.966A  pdb=" N   ARG B 261 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU B 262 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 286
      removed outlier: 3.967A  pdb=" N   SER B 284 " --> pdb=" O   TYR B 281 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   THR B 285 " --> pdb=" O   SER B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 303
    Processing helix  chain 'B' and resid 314 through 323
      removed outlier: 3.523A  pdb=" N   TYR B 318 " --> pdb=" O   VAL B 314 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLU B 323 " --> pdb=" O   GLN B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 349
    Processing helix  chain 'H' and resid 168 through 170
      No H-bonds generated for 'chain 'H' and resid 168 through 170'
    Processing helix  chain 'L' and resid 121 through 128
    Processing helix  chain 'L' and resid 183 through 188
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12
      removed outlier: 6.358A  pdb=" N   ASP A 434 " --> pdb=" O   ALA A 424 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ALA A 424 " --> pdb=" O   ASP A 434 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   SER A 420 " --> pdb=" O   GLY A 438 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27
    Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 79
      removed outlier: 3.546A  pdb=" N   GLU A  75 " --> pdb=" O   THR A  86 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 100
      removed outlier: 3.702A  pdb=" N   SER A  96 " --> pdb=" O   CYS A 107 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 175
    Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242
      removed outlier: 6.508A  pdb=" N   VAL A 267 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ARG A 279 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ILE A 269 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296
    Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315
    Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 364
      removed outlier: 5.983A  pdb=" N   ASP A 373 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLN A 405 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 394 through 395
    Processing sheet with id=AB2, first strand: chain 'B' and resid 60 through 65
      removed outlier: 6.352A  pdb=" N   ARG B  87 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 83 through 84
    Processing sheet with id=AB4, first strand: chain 'B' and resid 190 through 197
      removed outlier: 5.514A  pdb=" N   HIS B 192 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   ALA B 155 " --> pdb=" O   HIS B 192 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   LEU B 196 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
      removed outlier: 5.657A  pdb=" N   ILE B 151 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP B 119 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 8.879A  pdb=" N   THR B 329 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   LEU B 306 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   GLY B 331 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   PHE B 308 " --> pdb=" O   GLY B 331 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.346A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 122 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   MET H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   ARG H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   SER H  40 " --> pdb=" O   SER H  44 " (cutoff:3.500A)
      removed outlier: 5.701A  pdb=" N   SER H  44 " --> pdb=" O   SER H  40 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.346A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 122 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 132 through 136
      removed outlier: 6.151A  pdb=" N   TYR H 187 " --> pdb=" O   GLY H 156 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 132 through 136
      removed outlier: 6.151A  pdb=" N   TYR H 187 " --> pdb=" O   GLY H 156 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 163 through 166
    Processing sheet with id=AC2, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.589A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'L' and resid 114 through 118
      removed outlier: 3.535A  pdb=" N   VAL L 133 " --> pdb=" O   PHE L 118 " (cutoff:3.500A)
      removed outlier: 5.843A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'L' and resid 153 through 155
      removed outlier: 4.782A  pdb=" N   TRP L 148 " --> pdb=" O   ARG L 155 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   HIS L 198 " --> pdb=" O   SER L 203 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   SER L 203 " --> pdb=" O   HIS L 198 " (cutoff:3.500A)

    375 hydrogen bonds defined for protein.
    982 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: 3.85

  Time building geometry restraints manager: 2.85 seconds

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

  Histogram of bond lengths:
        0.91 -     1.10: 1
        1.10 -     1.30: 1634
        1.30 -     1.50: 4371
        1.50 -     1.70: 3962
        1.70 -     1.89: 62
  Bond restraints: 10030
  Sorted by residual:
  bond pdb=" CG  PRO A   5 "
       pdb=" CD  PRO A   5 "
    ideal  model  delta    sigma   weight residual
    1.503  0.908  0.595 3.40e-02 8.65e+02 3.07e+02
  bond pdb=" CB  PRO A   5 "
       pdb=" CG  PRO A   5 "
    ideal  model  delta    sigma   weight residual
    1.492  1.166  0.326 5.00e-02 4.00e+02 4.25e+01
  bond pdb=" N   PRO A   5 "
       pdb=" CA  PRO A   5 "
    ideal  model  delta    sigma   weight residual
    1.467  1.520 -0.053 1.17e-02 7.31e+03 2.06e+01
  bond pdb=" N   PRO A   5 "
       pdb=" CD  PRO A   5 "
    ideal  model  delta    sigma   weight residual
    1.473  1.416  0.057 1.40e-02 5.10e+03 1.63e+01
  bond pdb=" CA  PRO A   5 "
       pdb=" CB  PRO A   5 "
    ideal  model  delta    sigma   weight residual
    1.537  1.472  0.065 1.87e-02 2.86e+03 1.22e+01
  ... (remaining 10025 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.76: 13630
       14.76 -    29.52: 3
       29.52 -    44.28: 0
       44.28 -    59.04: 0
       59.04 -    73.79: 1
  Bond angle restraints: 13634
  Sorted by residual:
  angle pdb=" CB  PRO A   5 "
        pdb=" CG  PRO A   5 "
        pdb=" CD  PRO A   5 "
      ideal   model   delta    sigma   weight residual
     106.10  179.89  -73.79 3.20e+00 9.77e-02 5.32e+02
  angle pdb=" N   PRO A   5 "
        pdb=" CD  PRO A   5 "
        pdb=" CG  PRO A   5 "
      ideal   model   delta    sigma   weight residual
     103.20   80.54   22.66 1.50e+00 4.44e-01 2.28e+02
  angle pdb=" CA  PRO A   5 "
        pdb=" CB  PRO A   5 "
        pdb=" CG  PRO A   5 "
      ideal   model   delta    sigma   weight residual
     104.50   77.20   27.30 1.90e+00 2.77e-01 2.07e+02
  angle pdb=" CA  PRO A   5 "
        pdb=" N   PRO A   5 "
        pdb=" CD  PRO A   5 "
      ideal   model   delta    sigma   weight residual
     112.00  100.68   11.32 1.40e+00 5.10e-01 6.53e+01
  angle pdb=" C   ASP A   4 "
        pdb=" N   PRO A   5 "
        pdb=" CA  PRO A   5 "
      ideal   model   delta    sigma   weight residual
     120.47  112.23    8.24 1.07e+00 8.73e-01 5.94e+01
  ... (remaining 13629 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 5226
       17.70 -    35.39: 583
       35.39 -    53.09: 133
       53.09 -    70.78: 40
       70.78 -    88.48: 18
  Dihedral angle restraints: 6000
    sinusoidal: 2348
      harmonic: 3652
  Sorted by residual:
  dihedral pdb=" CA  PHE H 158 "
           pdb=" C   PHE H 158 "
           pdb=" N   PRO H 159 "
           pdb=" CA  PRO H 159 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -125.81  -54.19     0      5.00e+00 4.00e-02 1.17e+02
  dihedral pdb=" CA  GLU H 160 "
           pdb=" C   GLU H 160 "
           pdb=" N   PRO H 161 "
           pdb=" CA  PRO H 161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.73   42.27     0      5.00e+00 4.00e-02 7.15e+01
  dihedral pdb=" CB  CYS A 107 "
           pdb=" SG  CYS A 107 "
           pdb=" SG  CYS A 130 "
           pdb=" CB  CYS A 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   17.90   75.10     1      1.00e+01 1.00e-02 7.13e+01
  ... (remaining 5997 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1074
       0.042 -    0.085: 297
       0.085 -    0.127: 114
       0.127 -    0.170: 10
       0.170 -    0.212: 2
  Chirality restraints: 1497
  Sorted by residual:
  chirality pdb=" CA  PRO A   5 "
            pdb=" N   PRO A   5 "
            pdb=" C   PRO A   5 "
            pdb=" CB  PRO A   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.93   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  CYS A 130 "
            pdb=" N   CYS A 130 "
            pdb=" C   CYS A 130 "
            pdb=" CB  CYS A 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.70e-01
  chirality pdb=" CB  VAL B 314 "
            pdb=" CA  VAL B 314 "
            pdb=" CG1 VAL B 314 "
            pdb=" CG2 VAL B 314 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.48e-01
  ... (remaining 1494 not shown)

  Planarity restraints: 1776
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A   4 "    0.085 5.00e-02 4.00e+02   1.20e-01 2.30e+01
        pdb=" N   PRO A   5 "   -0.206 5.00e-02 4.00e+02
        pdb=" CA  PRO A   5 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A   5 "    0.074 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 158 "   -0.066 5.00e-02 4.00e+02   1.01e-01 1.63e+01
        pdb=" N   PRO H 159 "    0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO H 159 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO H 159 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS H 211 "   -0.042 5.00e-02 4.00e+02   6.41e-02 6.57e+00
        pdb=" N   PRO H 212 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO H 212 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO H 212 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1773 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 81
        2.56 -     3.15: 7123
        3.15 -     3.73: 14099
        3.73 -     4.32: 21425
        4.32 -     4.90: 36571
  Nonbonded interactions: 79299
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 123 "
            pdb="MG    MG B 801 "
     model   vdw
     1.978 2.170
  nonbonded pdb=" OD1 ASP A 434 "
            pdb="CA    CA A1104 "
     model   vdw
     2.179 2.510
  nonbonded pdb=" NH1 ARG L  61 "
            pdb=" OD2 ASP L  82 "
     model   vdw
     2.183 3.120
  nonbonded pdb=" OH  TYR A 288 "
            pdb=" OD1 ASP B 259 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OD1 ASP A 373 "
            pdb="CA    CA A1103 "
     model   vdw
     2.210 2.510
  ... (remaining 79294 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             6.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     32.590
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
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      :  0.008   0.595  10040  Z= 0.248
  Angle     :  0.966  73.794  13654  Z= 0.446
  Chirality :  0.045   0.212   1497
  Planarity :  0.006   0.120   1776
  Dihedral  : 16.573  88.480   3644
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.48 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 20.65 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.99 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.24), residues: 1261
  helix: -0.75 (0.48), residues: 116
  sheet:  1.13 (0.24), residues: 489
  loop : -1.33 (0.23), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 113 
 HIS   0.004   0.001   HIS A 215 
 PHE   0.020   0.002   PHE A  19 
 TYR   0.011   0.001   TYR A 448 
 ARG   0.003   0.000   ARG B 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13057 (  356)
  hydrogen bonds       : angle       7.32529 (  982)
  SS BOND              : bond        0.00797 (   10)
  SS BOND              : angle       2.56259 (   20)
  covalent geometry    : bond        0.00756 (10030)
  covalent geometry    : angle       0.96171 (13634)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 1.044 
Fit side-chains
REVERT: A  275 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6964 (mp10)
REVERT: H   10 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7135 (mm-30)
  outliers start: 24
  outliers final: 20
  residues processed: 108
  average time/residue: 1.4046
  time to fit residues: 161.9519
Evaluate side-chains
  107 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   43 LYS
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  176 HIS
Chi-restraints excluded: chain H residue  216 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   61 ARG
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  133 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 97 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0070
   chunk 72 optimal weight:    0.9980
   chunk 113 optimal weight:    0.4980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
A 111 GLN
A 215 HIS
A 333 GLN
A 405 GLN
B 342 GLN
H  52 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.199970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.155297 restraints weight = 24736.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 8.66
r_work: 0.3116 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3090
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.0542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084  10040  Z= 0.133
  Angle     :  0.649  14.765  13654  Z= 0.333
  Chirality :  0.045   0.145   1497
  Planarity :  0.005   0.100   1776
  Dihedral  :  6.686  72.771   1428
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.00 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.17 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.99 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.24), residues: 1261
  helix: -0.34 (0.48), residues: 116
  sheet:  0.97 (0.24), residues: 503
  loop : -1.28 (0.23), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 113 
 HIS   0.003   0.001   HIS A 215 
 PHE   0.020   0.002   PHE A  19 
 TYR   0.012   0.001   TYR B 348 
 ARG   0.004   0.000   ARG H 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03371 (  356)
  hydrogen bonds       : angle       5.90382 (  982)
  SS BOND              : bond        0.00789 (   10)
  SS BOND              : angle       2.33915 (   20)
  covalent geometry    : bond        0.00328 (10030)
  covalent geometry    : angle       0.64309 (13634)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.982 
Fit side-chains
REVERT: B  323 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.6695 (mp0)
REVERT: H    5 ARG cc_start: 0.7180 (ttp-170) cc_final: 0.6874 (mtm180)
REVERT: L   60 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7428 (mptt)
  outliers start: 30
  outliers final: 11
  residues processed: 115
  average time/residue: 1.3330
  time to fit residues: 163.6466
Evaluate side-chains
  98 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain B residue  143 ARG
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  323 GLU
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  194 THR
Chi-restraints excluded: chain L residue   20 SER
Chi-restraints excluded: chain L residue   60 LYS
Chi-restraints excluded: chain L residue  133 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 40 optimal weight:    0.1980
   chunk 85 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 116 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0970
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
A 215 HIS
A 405 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.200442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.152770 restraints weight = 22002.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 5.13
r_work: 0.3307 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3247
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3247
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.0741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089  10040  Z= 0.147
  Angle     :  0.632  15.911  13654  Z= 0.323
  Chirality :  0.046   0.167   1497
  Planarity :  0.005   0.101   1776
  Dihedral  :  5.349  53.054   1397
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.00 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 18.89 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.99 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.24), residues: 1261
  helix: -0.22 (0.49), residues: 116
  sheet:  0.96 (0.24), residues: 507
  loop : -1.31 (0.23), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 238 
 HIS   0.004   0.001   HIS A 215 
 PHE   0.024   0.002   PHE A  19 
 TYR   0.012   0.001   TYR B 318 
 ARG   0.003   0.000   ARG H 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03417 (  356)
  hydrogen bonds       : angle       5.70723 (  982)
  SS BOND              : bond        0.00883 (   10)
  SS BOND              : angle       2.57462 (   20)
  covalent geometry    : bond        0.00360 (10030)
  covalent geometry    : angle       0.62483 (13634)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 84
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A  121 GLU cc_start: 0.7783 (pt0) cc_final: 0.7553 (pt0)
REVERT: A  275 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7260 (mp10)
REVERT: A  280 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8501 (mt)
REVERT: A  288 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7889 (m-80)
REVERT: A  395 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8068 (pm20)
REVERT: B  323 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.6762 (mp0)
REVERT: H    5 ARG cc_start: 0.7321 (ttp-170) cc_final: 0.7119 (mtm110)
REVERT: L   60 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7458 (mptt)
REVERT: L  108 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7967 (ppt170)
  outliers start: 36
  outliers final: 14
  residues processed: 115
  average time/residue: 1.3421
  time to fit residues: 164.8569
Evaluate side-chains
  105 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  395 GLN
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  323 GLU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  194 THR
Chi-restraints excluded: chain L residue   20 SER
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   60 LYS
Chi-restraints excluded: chain L residue  108 ARG
Chi-restraints excluded: chain L residue  133 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 112 optimal weight:    2.9990
   chunk 121 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 95 optimal weight:    9.9990
   chunk 23 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 78 optimal weight:   10.0000
   chunk 94 optimal weight:    4.9990
   chunk 39 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
A 215 HIS
A 405 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.197735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.149915 restraints weight = 28509.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 5.58
r_work: 0.3085 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3193
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.0954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091  10040  Z= 0.166
  Angle     :  0.659  17.473  13654  Z= 0.336
  Chirality :  0.047   0.197   1497
  Planarity :  0.005   0.099   1776
  Dihedral  :  5.491  55.147   1397
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.24 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 18.89 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.99 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.24), residues: 1261
  helix: -0.24 (0.48), residues: 116
  sheet:  0.87 (0.24), residues: 511
  loop : -1.35 (0.23), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 238 
 HIS   0.004   0.001   HIS A 215 
 PHE   0.026   0.002   PHE A  19 
 TYR   0.012   0.002   TYR B 318 
 ARG   0.002   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03475 (  356)
  hydrogen bonds       : angle       5.66446 (  982)
  SS BOND              : bond        0.00907 (   10)
  SS BOND              : angle       2.69024 (   20)
  covalent geometry    : bond        0.00409 (10030)
  covalent geometry    : angle       0.65187 (13634)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 90
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A  121 GLU cc_start: 0.7841 (pt0) cc_final: 0.7604 (pt0)
REVERT: A  140 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7754 (mmt-90)
REVERT: A  158 ASN cc_start: 0.6887 (m-40) cc_final: 0.6643 (m110)
REVERT: A  275 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7069 (mp10)
REVERT: A  280 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8396 (mt)
REVERT: A  288 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.7864 (m-80)
REVERT: A  395 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.8003 (pm20)
REVERT: B  143 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7521 (mmt-90)
REVERT: B  348 TYR cc_start: 0.5382 (t80) cc_final: 0.4404 (t80)
REVERT: H    5 ARG cc_start: 0.7275 (ttp-170) cc_final: 0.6967 (mtm110)
REVERT: L   60 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7635 (mptt)
  outliers start: 36
  outliers final: 14
  residues processed: 117
  average time/residue: 1.2546
  time to fit residues: 157.5037
Evaluate side-chains
  111 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ARG
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  395 GLN
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue  143 ARG
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  194 THR
Chi-restraints excluded: chain L residue   20 SER
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   60 LYS
Chi-restraints excluded: chain L residue  133 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0000
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS
A 299 ASN
A 405 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.198903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.155822 restraints weight = 26090.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 5.17
r_work: 0.3249 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3265
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3265
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083  10040  Z= 0.134
  Angle     :  0.612  15.310  13654  Z= 0.313
  Chirality :  0.045   0.160   1497
  Planarity :  0.005   0.097   1776
  Dihedral  :  5.360  53.917   1397
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.08 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 20.00 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.99 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.24), residues: 1261
  helix: -0.14 (0.48), residues: 118
  sheet:  0.91 (0.24), residues: 500
  loop : -1.29 (0.23), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 113 
 HIS   0.003   0.001   HIS A 215 
 PHE   0.020   0.002   PHE A  19 
 TYR   0.018   0.001   TYR B 110 
 ARG   0.002   0.000   ARG H 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03087 (  356)
  hydrogen bonds       : angle       5.55001 (  982)
  SS BOND              : bond        0.00872 (   10)
  SS BOND              : angle       2.49058 (   20)
  covalent geometry    : bond        0.00327 (10030)
  covalent geometry    : angle       0.60511 (13634)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 1.064 
Fit side-chains
REVERT: A  121 GLU cc_start: 0.7884 (pt0) cc_final: 0.7667 (pt0)
REVERT: A  140 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7895 (mmt-90)
REVERT: A  243 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.6924 (tm-30)
REVERT: A  275 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7157 (mp10)
REVERT: A  280 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8496 (mt)
REVERT: A  288 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7757 (m-80)
REVERT: B  206 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8264 (tp30)
REVERT: B  348 TYR cc_start: 0.5560 (t80) cc_final: 0.4674 (t80)
REVERT: H    5 ARG cc_start: 0.7350 (ttp-170) cc_final: 0.7093 (mtm110)
REVERT: L   41 ASP cc_start: 0.7235 (t70) cc_final: 0.7000 (t0)
REVERT: L   60 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7464 (mptt)
  outliers start: 31
  outliers final: 15
  residues processed: 120
  average time/residue: 1.3643
  time to fit residues: 174.7900
Evaluate side-chains
  114 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ARG
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  177 CYS
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  194 THR
Chi-restraints excluded: chain L residue   20 SER
Chi-restraints excluded: chain L residue   60 LYS
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  175 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 120 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 94 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0470
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.7482

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
A 215 HIS
A 405 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.198538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.153442 restraints weight = 20699.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 4.40
r_work: 0.3351 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085  10040  Z= 0.137
  Angle     :  0.618  16.734  13654  Z= 0.315
  Chirality :  0.045   0.185   1497
  Planarity :  0.005   0.097   1776
  Dihedral  :  5.346  53.740   1397
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.16 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 18.98 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.99 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.24), residues: 1261
  helix: -0.05 (0.48), residues: 118
  sheet:  0.94 (0.24), residues: 500
  loop : -1.29 (0.23), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 113 
 HIS   0.004   0.001   HIS A 215 
 PHE   0.022   0.002   PHE A  19 
 TYR   0.011   0.001   TYR B 318 
 ARG   0.002   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03123 (  356)
  hydrogen bonds       : angle       5.49503 (  982)
  SS BOND              : bond        0.00877 (   10)
  SS BOND              : angle       2.51596 (   20)
  covalent geometry    : bond        0.00335 (10030)
  covalent geometry    : angle       0.61140 (13634)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 91
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 GLU cc_start: 0.7792 (pt0) cc_final: 0.7581 (pt0)
REVERT: A  140 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7885 (mmt-90)
REVERT: A  243 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.6863 (tm-30)
REVERT: A  275 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7084 (mp10)
REVERT: A  280 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8482 (mt)
REVERT: A  288 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7852 (m-80)
REVERT: B  143 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7424 (mmt-90)
REVERT: B  348 TYR cc_start: 0.5338 (t80) cc_final: 0.4660 (t80)
REVERT: B  387 MET cc_start: 0.7274 (mmp) cc_final: 0.7030 (mtt)
REVERT: L   41 ASP cc_start: 0.7219 (t70) cc_final: 0.6995 (t0)
REVERT: L   60 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7524 (mptt)
  outliers start: 36
  outliers final: 21
  residues processed: 118
  average time/residue: 1.2542
  time to fit residues: 158.5021
Evaluate side-chains
  120 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ARG
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue  143 ARG
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  177 CYS
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  323 GLU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   20 SER
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   60 LYS
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  175 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0370
   chunk 111 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A   7 GLN
A 215 HIS
B  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.199156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.161684 restraints weight = 24468.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 3.63
r_work: 0.3280 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3295
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3295
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083  10040  Z= 0.125
  Angle     :  0.604  15.778  13654  Z= 0.307
  Chirality :  0.045   0.174   1497
  Planarity :  0.005   0.096   1776
  Dihedral  :  5.278  52.972   1397
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.24 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.63 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.99 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.24), residues: 1261
  helix:  0.07 (0.48), residues: 118
  sheet:  0.95 (0.24), residues: 500
  loop : -1.27 (0.23), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 113 
 HIS   0.004   0.001   HIS A 215 
 PHE   0.020   0.002   PHE A  19 
 TYR   0.011   0.001   TYR B 318 
 ARG   0.006   0.000   ARG B 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02984 (  356)
  hydrogen bonds       : angle       5.43532 (  982)
  SS BOND              : bond        0.00829 (   10)
  SS BOND              : angle       2.42283 (   20)
  covalent geometry    : bond        0.00307 (10030)
  covalent geometry    : angle       0.59683 (13634)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 87
  time to evaluate  : 0.976 
Fit side-chains
REVERT: A  140 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7881 (mmt-90)
REVERT: A  243 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.6847 (tm-30)
REVERT: A  275 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7109 (mp10)
REVERT: A  280 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8498 (mt)
REVERT: A  288 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.7851 (m-80)
REVERT: B  143 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7397 (mmt-90)
REVERT: B  348 TYR cc_start: 0.5413 (t80) cc_final: 0.4756 (t80)
REVERT: B  387 MET cc_start: 0.7287 (mmp) cc_final: 0.6974 (mtt)
REVERT: L   60 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7446 (mptt)
  outliers start: 34
  outliers final: 18
  residues processed: 111
  average time/residue: 1.3216
  time to fit residues: 156.7268
Evaluate side-chains
  111 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ARG
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue  143 ARG
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  177 CYS
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   20 SER
Chi-restraints excluded: chain L residue   60 LYS
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  175 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 57 optimal weight:    0.2980
   chunk 87 optimal weight:    0.0070
   chunk 79 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 99 optimal weight:    7.9990
   chunk 19 optimal weight:    0.0570
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.199045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.154409 restraints weight = 25736.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 7.53
r_work: 0.3059 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083  10040  Z= 0.128
  Angle     :  0.606  15.513  13654  Z= 0.309
  Chirality :  0.045   0.168   1497
  Planarity :  0.005   0.096   1776
  Dihedral  :  5.265  52.856   1397
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.24 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.00 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.99 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.24), residues: 1261
  helix:  0.15 (0.48), residues: 118
  sheet:  0.96 (0.24), residues: 500
  loop : -1.26 (0.23), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 113 
 HIS   0.004   0.001   HIS A 215 
 PHE   0.020   0.002   PHE A  19 
 TYR   0.011   0.001   TYR B 318 
 ARG   0.007   0.000   ARG B 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03004 (  356)
  hydrogen bonds       : angle       5.40697 (  982)
  SS BOND              : bond        0.00826 (   10)
  SS BOND              : angle       2.42130 (   20)
  covalent geometry    : bond        0.00314 (10030)
  covalent geometry    : angle       0.59901 (13634)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 86
  time to evaluate  : 1.056 
Fit side-chains
REVERT: A  121 GLU cc_start: 0.8046 (pt0) cc_final: 0.7515 (pp20)
REVERT: A  140 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7780 (mmt-90)
REVERT: A  243 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.6834 (tm-30)
REVERT: A  275 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6906 (mp10)
REVERT: A  280 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8355 (mt)
REVERT: A  288 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7779 (m-80)
REVERT: B  143 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7257 (mmt-90)
REVERT: B  206 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8170 (tp30)
REVERT: B  387 MET cc_start: 0.7080 (mmp) cc_final: 0.6779 (mtt)
REVERT: L   60 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7644 (mptt)
  outliers start: 29
  outliers final: 18
  residues processed: 110
  average time/residue: 1.3849
  time to fit residues: 162.5837
Evaluate side-chains
  109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ARG
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue  143 ARG
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  177 CYS
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   20 SER
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   60 LYS
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  175 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 115 optimal weight:    8.9990
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 51 optimal weight:    0.6980
   chunk 1 optimal weight:    0.4980
   chunk 77 optimal weight:    8.9990
   chunk 31 optimal weight:    0.0060
   chunk 72 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0570
   overall best weight:    0.3714

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
A 215 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.201101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.154520 restraints weight = 29350.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 5.92
r_work: 0.3132 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.072  10040  Z= 0.101
  Angle     :  0.567  15.326  13654  Z= 0.289
  Chirality :  0.043   0.177   1497
  Planarity :  0.005   0.095   1776
  Dihedral  :  5.055  50.973   1397
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.24 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 20.83 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.99 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.24), residues: 1261
  helix:  0.31 (0.49), residues: 118
  sheet:  1.07 (0.24), residues: 494
  loop : -1.23 (0.23), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 113 
 HIS   0.004   0.001   HIS A 215 
 PHE   0.016   0.001   PHE L  91 
 TYR   0.011   0.001   TYR A 448 
 ARG   0.007   0.000   ARG B 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02646 (  356)
  hydrogen bonds       : angle       5.27390 (  982)
  SS BOND              : bond        0.00879 (   10)
  SS BOND              : angle       2.15588 (   20)
  covalent geometry    : bond        0.00244 (10030)
  covalent geometry    : angle       0.56131 (13634)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 1.091 
Fit side-chains
REVERT: A  121 GLU cc_start: 0.7986 (pt0) cc_final: 0.7391 (pp20)
REVERT: A  288 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7524 (m-80)
REVERT: B  143 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7316 (mmt-90)
REVERT: B  387 MET cc_start: 0.7211 (mmp) cc_final: 0.6884 (mtt)
REVERT: H   13 LYS cc_start: 0.7936 (mppt) cc_final: 0.7455 (mmmt)
REVERT: L   60 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7611 (mptt)
  outliers start: 22
  outliers final: 13
  residues processed: 106
  average time/residue: 1.3131
  time to fit residues: 149.9934
Evaluate side-chains
  103 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 1.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain B residue  143 ARG
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  177 CYS
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   20 SER
Chi-restraints excluded: chain L residue   60 LYS
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  175 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 95 optimal weight:    9.9990
   chunk 111 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 110 optimal weight:    0.4980
   chunk 99 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.197627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.147494 restraints weight = 26446.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 6.22
r_work: 0.3076 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.094  10040  Z= 0.195
  Angle     :  0.693  18.139  13654  Z= 0.351
  Chirality :  0.048   0.215   1497
  Planarity :  0.006   0.099   1776
  Dihedral  :  5.518  54.661   1397
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.56 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 21.02 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.96 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.99 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.23), residues: 1261
  helix:  0.12 (0.48), residues: 116
  sheet:  0.95 (0.24), residues: 503
  loop : -1.30 (0.23), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 238 
 HIS   0.005   0.001   HIS A 215 
 PHE   0.029   0.002   PHE A  19 
 TYR   0.014   0.002   TYR B 116 
 ARG   0.007   0.001   ARG B 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03610 (  356)
  hydrogen bonds       : angle       5.52164 (  982)
  SS BOND              : bond        0.01010 (   10)
  SS BOND              : angle       2.87378 (   20)
  covalent geometry    : bond        0.00486 (10030)
  covalent geometry    : angle       0.68427 (13634)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 1.089 
Fit side-chains
REVERT: A  275 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6792 (mp10)
REVERT: A  280 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8349 (mt)
REVERT: B  143 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7304 (mmt-90)
REVERT: B  387 MET cc_start: 0.7248 (mmp) cc_final: 0.6904 (mtt)
REVERT: L   41 ASP cc_start: 0.7356 (t70) cc_final: 0.7078 (t0)
REVERT: L   60 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7706 (mptt)
  outliers start: 19
  outliers final: 12
  residues processed: 105
  average time/residue: 1.2669
  time to fit residues: 142.8000
Evaluate side-chains
  103 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain B residue  143 ARG
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   20 SER
Chi-restraints excluded: chain L residue   60 LYS
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  175 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 72.9324 > 50:
  distance: 37 - 123:  32.974
  distance: 40 - 120:  34.102
  distance: 50 - 108:  37.579
  distance: 53 - 105:  34.818
  distance: 65 - 98:  36.723
  distance: 68 - 95:  33.997
  distance: 82 - 87:  35.356
  distance: 87 - 88:  55.846
  distance: 87 - 238:  35.487
  distance: 88 - 89:  40.717
  distance: 88 - 91:  40.543
  distance: 89 - 90:  39.186
  distance: 89 - 95:  69.503
  distance: 90 - 235:  37.323
  distance: 91 - 92:  67.927
  distance: 92 - 93:  56.523
  distance: 92 - 94:  55.472
  distance: 96 - 97:  56.593
  distance: 97 - 98:  40.509
  distance: 97 - 99:  68.647
  distance: 99 - 100:  38.591
  distance: 99 - 227:  36.582
  distance: 100 - 101:  38.575
  distance: 100 - 103:  70.636
  distance: 101 - 102:  38.984
  distance: 101 - 105:  40.236
  distance: 102 - 224:  37.421
  distance: 103 - 104:  38.382
  distance: 104 - 259:  34.251
  distance: 105 - 106:  40.327
  distance: 106 - 107:  69.627
  distance: 106 - 109:  39.084
  distance: 107 - 108:  68.302
  distance: 107 - 113:  56.517
  distance: 109 - 110:  58.000
  distance: 110 - 111:  55.122
  distance: 110 - 112:  56.671
  distance: 113 - 114:  40.312
  distance: 113 - 214:  33.258
  distance: 114 - 115:  57.423
  distance: 115 - 116:  56.056
  distance: 115 - 120:  56.276
  distance: 116 - 211:  35.750
  distance: 117 - 118:  57.997
  distance: 117 - 119:  67.892
  distance: 120 - 121:  41.101
  distance: 121 - 122:  40.126
  distance: 121 - 124:  39.180
  distance: 122 - 123:  56.937
  distance: 122 - 129:  40.604
  distance: 124 - 125:  57.435
  distance: 125 - 126:  58.067
  distance: 126 - 127:  40.060
  distance: 127 - 128:  57.255
  distance: 129 - 130:  39.794
  distance: 129 - 200:  32.253
  distance: 131 - 132:  57.600
  distance: 131 - 133:  68.440
  distance: 133 - 134:  39.337
  distance: 134 - 135:  56.540
  distance: 134 - 137:  39.705
  distance: 135 - 136:  56.917
  distance: 135 - 145:  40.179
  distance: 137 - 138:  57.616
  distance: 138 - 139:  67.967
  distance: 138 - 140:  69.743
  distance: 141 - 143:  55.507
  distance: 142 - 143:  57.636
  distance: 143 - 144:  56.510
  distance: 146 - 147:  68.976
  distance: 146 - 149:  68.849
  distance: 147 - 148:  40.092
  distance: 149 - 150:  38.596
  distance: 150 - 151:  40.192
  distance: 150 - 152:  40.914
  distance: 151 - 153:  55.847
  distance: 152 - 154:  55.804
  distance: 153 - 155:  39.155
  distance: 154 - 155:  41.306
  distance: 156 - 162:  57.792
  distance: 157 - 158:  40.830
  distance: 157 - 160:  38.728
  distance: 158 - 159:  39.154
  distance: 158 - 163:  34.879
  distance: 160 - 161:  40.342
  distance: 161 - 162:  55.670