Starting phenix.real_space_refine
on Sun Jun  8 18:42:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dao_46695/06_2025/9dao_46695_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dao_46695/06_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_46695/06_2025/9dao_46695.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dao_46695/06_2025/9dao_46695.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dao_46695/06_2025/9dao_46695_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dao_46695/06_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-5710/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: 11.10, per 1000 atoms: 1.13
  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: 2.27
  Conformation dependent library (CDL) restraints added in 2.3 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: 1.49
  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: 3.31

  Time building geometry restraints manager: 2.74 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:             5.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     32.770
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:13.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.740
-------------------------------------------------------------------------------
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  : 1.073 
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: 1.4637
  time to fit residues: 168.8212
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  : 1.002 
-------------------------------------------------------------------------------
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 = 0.199966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.158972 restraints weight = 24736.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 4.18
r_work: 0.3289 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3271
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    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 = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3270
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
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        0.03372 (  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  : 1.212 
Fit side-chains
REVERT: B  323 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.6814 (mp0)
REVERT: H    5 ARG cc_start: 0.7272 (ttp-170) cc_final: 0.7064 (mtm180)
REVERT: L   60 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7413 (mptt)
  outliers start: 30
  outliers final: 11
  residues processed: 115
  average time/residue: 1.4546
  time to fit residues: 178.8461
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  : 0.989 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 116 optimal weight:    8.9990
   chunk 31 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   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 = 0.197852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.151558 restraints weight = 22626.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 8.07
r_work: 0.3099 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3232
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3232
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.0812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.092  10040  Z= 0.167
  Angle     :  0.664  16.717  13654  Z= 0.338
  Chirality :  0.047   0.178   1497
  Planarity :  0.006   0.101   1776
  Dihedral  :  5.499  54.199   1397
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.24 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 18.89 %
    Favored  : 77.31 %
  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: -0.42 (0.24), residues: 1261
  helix: -0.29 (0.48), residues: 116
  sheet:  0.96 (0.24), residues: 506
  loop : -1.35 (0.23), residues: 639

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   0.027   0.002   PHE A  19 
 TYR   0.012   0.002   TYR B 318 
 ARG   0.003   0.000   ARG H 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03624 (  356)
  hydrogen bonds       : angle       5.75977 (  982)
  SS BOND              : bond        0.00885 (   10)
  SS BOND              : angle       2.69760 (   20)
  covalent geometry    : bond        0.00410 (10030)
  covalent geometry    : angle       0.65602 (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: 37
    poor density    : 83
  time to evaluate  : 0.988 
Fit side-chains
REVERT: A  121 GLU cc_start: 0.7768 (pt0) cc_final: 0.7511 (pt0)
REVERT: A  275 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6977 (mp10)
REVERT: A  280 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8326 (mt)
REVERT: A  395 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7918 (pm20)
REVERT: B  323 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.6600 (mp0)
REVERT: B  387 MET cc_start: 0.6815 (mtt) cc_final: 0.6557 (mmp)
REVERT: H    5 ARG cc_start: 0.7166 (ttp-170) cc_final: 0.6846 (mtm110)
REVERT: L   60 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7613 (mptt)
  outliers start: 37
  outliers final: 14
  residues processed: 114
  average time/residue: 1.5318
  time to fit residues: 186.4409
Evaluate side-chains
  102 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 1.616 
-------------------------------------------------------------------------------
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 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  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:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 94 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0370
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.4066

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.196965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.146334 restraints weight = 28324.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 6.73
r_work: 0.3083 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.101         |
| 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) = 0.101         |
| 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: 0.8273
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.098  10040  Z= 0.212
  Angle     :  0.725  19.123  13654  Z= 0.368
  Chirality :  0.049   0.214   1497
  Planarity :  0.006   0.099   1776
  Dihedral  :  5.810  57.870   1397
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.72 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 18.43 %
    Favored  : 76.94 %
  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: -0.61 (0.23), residues: 1261
  helix: -0.56 (0.47), residues: 116
  sheet:  0.79 (0.24), residues: 503
  loop : -1.40 (0.23), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 238 
 HIS   0.004   0.001   HIS A 215 
 PHE   0.032   0.002   PHE A  19 
 TYR   0.015   0.002   TYR B 116 
 ARG   0.003   0.000   ARG B 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03894 (  356)
  hydrogen bonds       : angle       5.81484 (  982)
  SS BOND              : bond        0.01119 (   10)
  SS BOND              : angle       3.02792 (   20)
  covalent geometry    : bond        0.00524 (10030)
  covalent geometry    : angle       0.71605 (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
  138 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 94
  time to evaluate  : 1.149 
Fit side-chains
REVERT: A  121 GLU cc_start: 0.7916 (pt0) cc_final: 0.7676 (pt0)
REVERT: A  140 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7684 (tpp-160)
REVERT: A  158 ASN cc_start: 0.7121 (m-40) cc_final: 0.6918 (m110)
REVERT: A  243 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7347 (tm-30)
REVERT: A  275 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7067 (mp10)
REVERT: A  280 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8352 (mt)
REVERT: A  395 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.8004 (pm20)
REVERT: B  143 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7501 (mmt-90)
REVERT: B  348 TYR cc_start: 0.5360 (t80) cc_final: 0.4293 (t80)
REVERT: H    5 ARG cc_start: 0.7247 (ttp-170) cc_final: 0.6969 (mtm110)
REVERT: H   87 THR cc_start: 0.8566 (t) cc_final: 0.8302 (p)
REVERT: L   41 ASP cc_start: 0.7321 (t70) cc_final: 0.7012 (t70)
REVERT: L   60 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7646 (mptt)
REVERT: L   90 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7656 (pt0)
  outliers start: 44
  outliers final: 19
  residues processed: 131
  average time/residue: 1.3492
  time to fit residues: 189.1653
Evaluate side-chains
  119 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
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  348 THR
Chi-restraints excluded: chain A residue  395 GLN
Chi-restraints excluded: chain A residue  396 SER
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 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 H residue  176 HIS
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   90 GLN
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:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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
A 299 ASN
A 405 GLN
B  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.197182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.153505 restraints weight = 26316.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 5.19
r_work: 0.3219 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    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 = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.1216

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= 0.154
  Angle     :  0.645  16.738  13654  Z= 0.329
  Chirality :  0.046   0.181   1497
  Planarity :  0.005   0.098   1776
  Dihedral  :  5.600  55.701   1397
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.32 %
    Favored  : 95.52 %
  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: -0.51 (0.23), residues: 1261
  helix: -0.34 (0.47), residues: 116
  sheet:  0.84 (0.24), residues: 510
  loop : -1.38 (0.23), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 238 
 HIS   0.004   0.001   HIS A 215 
 PHE   0.023   0.002   PHE A  19 
 TYR   0.012   0.002   TYR B 318 
 ARG   0.002   0.000   ARG H 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03347 (  356)
  hydrogen bonds       : angle       5.65688 (  982)
  SS BOND              : bond        0.00890 (   10)
  SS BOND              : angle       2.67137 (   20)
  covalent geometry    : bond        0.00378 (10030)
  covalent geometry    : angle       0.63745 (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
  125 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 91
  time to evaluate  : 1.027 
Fit side-chains
REVERT: A  140 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7914 (mmt-90)
REVERT: A  158 ASN cc_start: 0.7006 (m-40) cc_final: 0.6729 (m110)
REVERT: A  275 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7235 (mp10)
REVERT: A  280 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8468 (mt)
REVERT: A  395 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8071 (pm20)
REVERT: B  323 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7361 (mp0)
REVERT: B  348 TYR cc_start: 0.5443 (t80) cc_final: 0.4566 (t80)
REVERT: H    5 ARG cc_start: 0.7409 (ttp-170) cc_final: 0.7117 (mtm110)
REVERT: L   60 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7629 (mptt)
  outliers start: 34
  outliers final: 18
  residues processed: 117
  average time/residue: 1.3121
  time to fit residues: 164.5379
Evaluate side-chains
  114 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
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  348 THR
Chi-restraints excluded: chain A residue  395 GLN
Chi-restraints excluded: chain A residue  396 SER
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  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   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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 117 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 94 optimal weight:    7.9990
   chunk 82 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   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 215 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.197408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.154196 restraints weight = 21075.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 4.16
r_work: 0.3301 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3286
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    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 = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3286
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090  10040  Z= 0.147
  Angle     :  0.640  17.600  13654  Z= 0.325
  Chirality :  0.046   0.209   1497
  Planarity :  0.005   0.098   1776
  Dihedral  :  5.502  54.827   1397
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.24 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.54 %
    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: -0.46 (0.24), residues: 1261
  helix: -0.23 (0.47), residues: 117
  sheet:  0.87 (0.24), residues: 507
  loop : -1.35 (0.23), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 235 
 HIS   0.004   0.001   HIS A 215 
 PHE   0.023   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        0.03249 (  356)
  hydrogen bonds       : angle       5.56139 (  982)
  SS BOND              : bond        0.00925 (   10)
  SS BOND              : angle       2.63449 (   20)
  covalent geometry    : bond        0.00361 (10030)
  covalent geometry    : angle       0.63277 (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: 35
    poor density    : 92
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7906 (mmt-90)
REVERT: A  243 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7020 (tm-30)
REVERT: A  275 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7133 (mp10)
REVERT: A  280 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8464 (mt)
REVERT: B  143 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7498 (mmt-90)
REVERT: B  348 TYR cc_start: 0.5508 (t80) cc_final: 0.4725 (t80)
REVERT: B  387 MET cc_start: 0.7366 (mmp) cc_final: 0.7073 (mtt)
REVERT: H    5 ARG cc_start: 0.7317 (ttp-170) cc_final: 0.7108 (mtm110)
  outliers start: 35
  outliers final: 18
  residues processed: 116
  average time/residue: 1.3376
  time to fit residues: 165.9341
Evaluate side-chains
  113 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
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  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  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   18 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue   20 SER
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:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 43 optimal weight:    0.3980
   chunk 91 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 104 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4182 r_free = 0.4182 target = 0.198326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.156011 restraints weight = 25012.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 4.94
r_work: 0.3264 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    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 = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1352

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= 0.128
  Angle     :  0.611  16.515  13654  Z= 0.311
  Chirality :  0.045   0.190   1497
  Planarity :  0.005   0.097   1776
  Dihedral  :  5.382  53.779   1397
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.32 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 20.09 %
    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: -0.41 (0.24), residues: 1261
  helix: -0.11 (0.48), residues: 118
  sheet:  0.90 (0.24), residues: 500
  loop : -1.31 (0.23), residues: 643

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   0.019   0.002   PHE A  19 
 TYR   0.012   0.001   TYR B 318 
 ARG   0.008   0.000   ARG B 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03022 (  356)
  hydrogen bonds       : angle       5.47930 (  982)
  SS BOND              : bond        0.00863 (   10)
  SS BOND              : angle       2.47347 (   20)
  covalent geometry    : bond        0.00312 (10030)
  covalent geometry    : angle       0.60371 (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
  117 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.988 
Fit side-chains
REVERT: A  140 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7915 (mmt-90)
REVERT: A  243 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.6885 (tm-30)
REVERT: A  275 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7115 (mp10)
REVERT: A  280 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8491 (mt)
REVERT: A  288 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.7731 (m-80)
REVERT: B  143 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7509 (mmt-90)
REVERT: B  348 TYR cc_start: 0.5406 (t80) cc_final: 0.4807 (t80)
REVERT: H    5 ARG cc_start: 0.7380 (ttp-170) cc_final: 0.7107 (mtm110)
REVERT: L  197 THR cc_start: 0.7267 (m) cc_final: 0.7058 (t)
  outliers start: 28
  outliers final: 14
  residues processed: 110
  average time/residue: 1.4168
  time to fit residues: 166.4591
Evaluate side-chains
  109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
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  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   33 LEU
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:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 24 optimal weight:    0.0870
   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:    0.0060
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.7976

-------------------------------------------------------------------------------
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 = 0.4178 r_free = 0.4178 target = 0.197801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.154274 restraints weight = 26409.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 5.21
r_work: 0.3257 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3248
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3248
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087  10040  Z= 0.142
  Angle     :  0.633  16.918  13654  Z= 0.321
  Chirality :  0.045   0.194   1497
  Planarity :  0.005   0.097   1776
  Dihedral  :  5.419  54.169   1397
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.24 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 20.37 %
    Favored  : 76.48 %
  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: -0.42 (0.24), residues: 1261
  helix: -0.09 (0.47), residues: 118
  sheet:  0.90 (0.24), residues: 500
  loop : -1.32 (0.23), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 113 
 HIS   0.005   0.001   HIS A 215 
 PHE   0.022   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        0.03174 (  356)
  hydrogen bonds       : angle       5.48499 (  982)
  SS BOND              : bond        0.00897 (   10)
  SS BOND              : angle       2.56848 (   20)
  covalent geometry    : bond        0.00349 (10030)
  covalent geometry    : angle       0.62566 (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
  118 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 90
  time to evaluate  : 1.073 
Fit side-chains
REVERT: A  140 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7921 (mmt-90)
REVERT: A  158 ASN cc_start: 0.7049 (m-40) cc_final: 0.6761 (m110)
REVERT: A  243 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.6946 (tm-30)
REVERT: A  275 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7088 (mp10)
REVERT: A  280 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8485 (mt)
REVERT: A  395 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.6463 (pt0)
REVERT: B  143 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7421 (mmt-90)
REVERT: B  348 TYR cc_start: 0.5438 (t80) cc_final: 0.4789 (t80)
REVERT: B  387 MET cc_start: 0.7337 (mmp) cc_final: 0.6932 (mtt)
REVERT: H    5 ARG cc_start: 0.7386 (ttp-170) cc_final: 0.7126 (mtm110)
REVERT: L  103 LYS cc_start: 0.8617 (ttpp) cc_final: 0.7923 (tttm)
  outliers start: 28
  outliers final: 17
  residues processed: 112
  average time/residue: 1.2515
  time to fit residues: 150.6961
Evaluate side-chains
  112 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
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  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  147 SER
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  211 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  332 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  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:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 81 optimal weight:    9.9990
   chunk 51 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   chunk 77 optimal weight:    0.0050
   chunk 31 optimal weight:    0.1980
   chunk 72 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.4596

-------------------------------------------------------------------------------
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 = 0.4195 r_free = 0.4195 target = 0.199822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.152424 restraints weight = 30504.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 7.08
r_work: 0.3140 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  10040  Z= 0.110
  Angle     :  0.586  15.549  13654  Z= 0.299
  Chirality :  0.044   0.173   1497
  Planarity :  0.005   0.095   1776
  Dihedral  :  5.206  52.359   1397
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.32 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.74 %
    Favored  : 76.39 %
  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: -0.31 (0.24), residues: 1261
  helix:  0.08 (0.48), residues: 118
  sheet:  0.95 (0.24), residues: 500
  loop : -1.25 (0.23), residues: 643

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   0.018   0.001   PHE L  91 
 TYR   0.011   0.001   TYR B 318 
 ARG   0.007   0.000   ARG B 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02797 (  356)
  hydrogen bonds       : angle       5.34957 (  982)
  SS BOND              : bond        0.00807 (   10)
  SS BOND              : angle       2.33209 (   20)
  covalent geometry    : bond        0.00266 (10030)
  covalent geometry    : angle       0.57989 (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
  109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 1.114 
Fit side-chains
REVERT: A  140 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7813 (mmt-90)
REVERT: B  143 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7259 (mmt-90)
REVERT: B  348 TYR cc_start: 0.5154 (t80) cc_final: 0.4616 (t80)
REVERT: B  387 MET cc_start: 0.7170 (mmp) cc_final: 0.6853 (mtt)
REVERT: H   13 LYS cc_start: 0.7905 (mppt) cc_final: 0.7440 (mmmt)
REVERT: L  103 LYS cc_start: 0.8494 (ttpp) cc_final: 0.7810 (tttm)
REVERT: L  108 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8257 (ptm160)
  outliers start: 25
  outliers final: 16
  residues processed: 102
  average time/residue: 1.3270
  time to fit residues: 145.6018
Evaluate side-chains
  101 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
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  182 VAL
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  177 CYS
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 B residue  332 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  108 ARG
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:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 95 optimal weight:   20.0000
   chunk 111 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 110 optimal weight:    0.8980
   chunk 99 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.4181 r_free = 0.4181 target = 0.197120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.147232 restraints weight = 27100.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 6.23
r_work: 0.3080 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3057
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3057 r_free = 0.3057    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3057 r_free = 0.3057    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3057
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.095  10040  Z= 0.206
  Angle     :  0.714  18.393  13654  Z= 0.362
  Chirality :  0.048   0.217   1497
  Planarity :  0.006   0.100   1776
  Dihedral  :  5.653  56.139   1397
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.40 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 20.74 %
    Favored  : 76.30 %
  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: -0.44 (0.24), residues: 1261
  helix: -0.13 (0.47), residues: 116
  sheet:  0.90 (0.24), residues: 510
  loop : -1.38 (0.23), residues: 635

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   0.030   0.002   PHE A  19 
 TYR   0.015   0.002   TYR B 116 
 ARG   0.007   0.000   ARG B 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03736 (  356)
  hydrogen bonds       : angle       5.61605 (  982)
  SS BOND              : bond        0.01058 (   10)
  SS BOND              : angle       3.10124 (   20)
  covalent geometry    : bond        0.00511 (10030)
  covalent geometry    : angle       0.70434 (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
  112 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 1.018 
Fit side-chains
REVERT: A  140 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7777 (mmt-90)
REVERT: A  275 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6789 (mp10)
REVERT: B  143 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7297 (mmt-90)
REVERT: B  387 MET cc_start: 0.7189 (mmp) cc_final: 0.6898 (mtt)
REVERT: H   13 LYS cc_start: 0.7970 (mppt) cc_final: 0.7498 (mmmt)
REVERT: L  108 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8293 (ptm160)
  outliers start: 26
  outliers final: 18
  residues processed: 107
  average time/residue: 1.2835
  time to fit residues: 147.2778
Evaluate side-chains
  108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
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  348 THR
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 B residue  315 VAL
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  108 ARG
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  197 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 79 optimal weight:    9.9990
   chunk 124 optimal weight:   10.0000
   chunk 107 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.197454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.150181 restraints weight = 29299.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 5.86
r_work: 0.3081 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.092  10040  Z= 0.161
  Angle     :  0.660  17.434  13654  Z= 0.336
  Chirality :  0.046   0.199   1497
  Planarity :  0.005   0.096   1776
  Dihedral  :  5.553  54.974   1397
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.40 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.93 %
    Favored  : 76.02 %
  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: -0.42 (0.24), residues: 1261
  helix: -0.13 (0.47), residues: 117
  sheet:  0.90 (0.24), residues: 510
  loop : -1.35 (0.23), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 238 
 HIS   0.005   0.001   HIS A 215 
 PHE   0.025   0.002   PHE A  19 
 TYR   0.012   0.002   TYR B 318 
 ARG   0.007   0.000   ARG B 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03336 (  356)
  hydrogen bonds       : angle       5.53072 (  982)
  SS BOND              : bond        0.00958 (   10)
  SS BOND              : angle       2.89880 (   20)
  covalent geometry    : bond        0.00398 (10030)
  covalent geometry    : angle       0.65122 (13634)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7967.05 seconds
wall clock time: 138 minutes 8.05 seconds (8288.05 seconds total)