Starting phenix.real_space_refine
on Thu Dec  7 18:24:57 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmc_25995/12_2023/7tmc_25995.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmc_25995/12_2023/7tmc_25995.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmc_25995/12_2023/7tmc_25995.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmc_25995/12_2023/7tmc_25995.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmc_25995/12_2023/7tmc_25995.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmc_25995/12_2023/7tmc_25995.pdb"
  }
  resolution = 3.25
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    2178      2.51       5
     N     531      2.21       5
     O     696      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP  122": "OD1" <-> "OD2"
    Residue "A TYR  125": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  161": "OE1" <-> "OE2"
    Residue "A GLU  163": "OE1" <-> "OE2"
    Residue "A ASP  191": "OD1" <-> "OD2"
    Residue "A GLU  246": "OE1" <-> "OE2"
    Residue "A TYR  250": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  252": "OD1" <-> "OD2"
    Residue "B TYR  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  161": "OE1" <-> "OE2"
    Residue "B TYR  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  237": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  122": "OD1" <-> "OD2"
    Residue "C TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 3426
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "C"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 2.42, per 1000 atoms: 0.71
  Number of scatterers: 3426
  At special positions: 0
  Unit cell: (101.184, 110.67, 35.836, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      21     16.00
     O     696      8.00
     N     531      7.00
     C    2178      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 301 " - " ASN A 151 "
      " NAG A 302 " - " ASN A 145 "
      " NAG A 303 " - " ASN A 164 "
      " NAG A 304 " - " ASN A 183 "
      " NAG B 301 " - " ASN B 151 "
      " NAG B 302 " - " ASN B 145 "
      " NAG B 303 " - " ASN B 164 "
      " NAG B 304 " - " ASN B 183 "
      " NAG C 301 " - " ASN C 151 "
      " NAG C 302 " - " ASN C 145 "
      " NAG C 303 " - " ASN C 164 "
      " NAG C 304 " - " ASN C 183 "
  Time building additional restraints: 1.33
  Conformation dependent library (CDL) restraints added in 587.7 milliseconds
  

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 17 sheets defined
      0.0% alpha, 44.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 124 through 126
      removed outlier: 6.091A  pdb=" N   TYR A 125 " --> pdb=" O   ILE C 126 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 130
      removed outlier: 8.001A  pdb=" N   SER B 134 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   VAL A 133 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 129 through 130
      removed outlier: 9.113A  pdb=" N   SER A 130 " --> pdb=" O   ALA C 131 " (cutoff:3.500A)
      removed outlier: 10.056A  pdb=" N   VAL C 133 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
      removed outlier: 5.916A  pdb=" N   TYR A 132 " --> pdb=" O   VAL C 133 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 143
      removed outlier: 5.870A  pdb=" N   ILE A 142 " --> pdb=" O   TYR C 143 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153
      removed outlier: 6.524A  pdb=" N   ILE A 152 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 157
      removed outlier: 6.522A  pdb=" N   ASN A 156 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 175
      removed outlier: 6.217A  pdb=" N   GLN A 170 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   LYS B 173 " --> pdb=" O   GLN A 170 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   SER A 172 " --> pdb=" O   LYS B 173 " (cutoff:3.500A)
      removed outlier: 8.219A  pdb=" N   VAL B 175 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   THR A 174 " --> pdb=" O   VAL B 175 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   VAL A 169 " --> pdb=" O   GLN C 170 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 175
      removed outlier: 6.217A  pdb=" N   GLN A 170 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   LYS B 173 " --> pdb=" O   GLN A 170 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   SER A 172 " --> pdb=" O   LYS B 173 " (cutoff:3.500A)
      removed outlier: 8.219A  pdb=" N   VAL B 175 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   THR A 174 " --> pdb=" O   VAL B 175 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 184 through 186
      removed outlier: 6.398A  pdb=" N   ILE A 184 " --> pdb=" O   THR B 185 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 190 through 193
      removed outlier: 6.878A  pdb=" N   LEU A 190 " --> pdb=" O   ASP B 191 " (cutoff:3.500A)
      removed outlier: 8.447A  pdb=" N   LYS B 193 " --> pdb=" O   LEU A 190 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   MET A 192 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 196 through 197
      removed outlier: 6.082A  pdb=" N   ASP A 196 " --> pdb=" O   TYR C 197 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 206
      removed outlier: 6.317A  pdb=" N   VAL A 202 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   GLU C 205 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ALA A 204 " --> pdb=" O   GLU C 205 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 209 through 218
      removed outlier: 6.767A  pdb=" N   MET A 210 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   PHE B 213 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ASP A 212 " --> pdb=" O   PHE B 213 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   THR B 215 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   CYS A 214 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
      removed outlier: 10.343A  pdb=" N   ILE B 217 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
      removed outlier: 9.147A  pdb=" N   LEU A 216 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   TYR A 209 " --> pdb=" O   MET C 210 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   ASP C 212 " --> pdb=" O   TYR A 209 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   TYR A 211 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 209 through 218
      removed outlier: 6.767A  pdb=" N   MET A 210 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   PHE B 213 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ASP A 212 " --> pdb=" O   PHE B 213 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   THR B 215 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   CYS A 214 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
      removed outlier: 10.343A  pdb=" N   ILE B 217 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
      removed outlier: 9.147A  pdb=" N   LEU A 216 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 224 through 228
      removed outlier: 6.060A  pdb=" N   VAL A 225 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   MET B 228 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   MET A 227 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 233 through 240
      removed outlier: 6.641A  pdb=" N   THR A 233 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   TYR B 236 " --> pdb=" O   THR A 233 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   THR A 235 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   GLY B 238 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   PHE A 237 " --> pdb=" O   GLY B 238 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   SER B 240 " --> pdb=" O   PHE A 237 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   HIS A 239 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 243 through 246
      removed outlier: 6.111A  pdb=" N   SER A 244 " --> pdb=" O   GLN C 245 " (cutoff:3.500A)

    37 hydrogen bonds defined for protein.
    111 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.79

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1050
        1.34 -     1.46: 802
        1.46 -     1.58: 1592
        1.58 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 3480
  Sorted by residual:
  bond pdb=" C1  NAG C 303 "
       pdb=" O5  NAG C 303 "
    ideal  model  delta    sigma   weight residual
    1.406  1.489 -0.083 2.00e-02 2.50e+03 1.71e+01
  bond pdb=" C1  NAG A 303 "
       pdb=" O5  NAG A 303 "
    ideal  model  delta    sigma   weight residual
    1.406  1.486 -0.080 2.00e-02 2.50e+03 1.60e+01
  bond pdb=" C1  NAG B 303 "
       pdb=" O5  NAG B 303 "
    ideal  model  delta    sigma   weight residual
    1.406  1.480 -0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" C1  NAG A 302 "
       pdb=" O5  NAG A 302 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.39e+00
  bond pdb=" C1  NAG C 302 "
       pdb=" O5  NAG C 302 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.34e+00
  ... (remaining 3475 not shown)

  Histogram of bond angle deviations from ideal:
      100.19 -   106.40: 59
      106.40 -   112.61: 1934
      112.61 -   118.81: 890
      118.81 -   125.02: 1837
      125.02 -   131.22: 11
  Bond angle restraints: 4731
  Sorted by residual:
  angle pdb=" N   GLY C 238 "
        pdb=" CA  GLY C 238 "
        pdb=" C   GLY C 238 "
      ideal   model   delta    sigma   weight residual
     110.29  114.60   -4.31 1.28e+00 6.10e-01 1.14e+01
  angle pdb=" N   ILE C 219 "
        pdb=" CA  ILE C 219 "
        pdb=" C   ILE C 219 "
      ideal   model   delta    sigma   weight residual
     109.34  103.85    5.49 2.08e+00 2.31e-01 6.96e+00
  angle pdb=" N   ILE A 219 "
        pdb=" CA  ILE A 219 "
        pdb=" C   ILE A 219 "
      ideal   model   delta    sigma   weight residual
     109.34  103.92    5.42 2.08e+00 2.31e-01 6.78e+00
  angle pdb=" N   GLN C 138 "
        pdb=" CA  GLN C 138 "
        pdb=" C   GLN C 138 "
      ideal   model   delta    sigma   weight residual
     109.65  113.65   -4.00 1.56e+00 4.11e-01 6.59e+00
  angle pdb=" N   ILE B 219 "
        pdb=" CA  ILE B 219 "
        pdb=" C   ILE B 219 "
      ideal   model   delta    sigma   weight residual
     109.34  104.08    5.26 2.08e+00 2.31e-01 6.40e+00
  ... (remaining 4726 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.85: 2092
       24.85 -    49.69: 114
       49.69 -    74.54: 27
       74.54 -    99.39: 7
       99.39 -   124.23: 7
  Dihedral angle restraints: 2247
    sinusoidal: 1029
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CB  CYS A 214 "
           pdb=" SG  CYS A 214 "
           pdb=" SG  CYS A 253 "
           pdb=" CB  CYS A 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.93  -74.93     1      1.00e+01 1.00e-02 7.10e+01
  dihedral pdb=" CB  CYS C 214 "
           pdb=" SG  CYS C 214 "
           pdb=" SG  CYS C 253 "
           pdb=" CB  CYS C 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.42  -70.42     1      1.00e+01 1.00e-02 6.38e+01
  dihedral pdb=" CA  TYR A 143 "
           pdb=" C   TYR A 143 "
           pdb=" N   LEU A 144 "
           pdb=" CA  LEU A 144 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.88  -25.12     0      5.00e+00 4.00e-02 2.52e+01
  ... (remaining 2244 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 491
       0.080 -    0.159: 102
       0.159 -    0.239: 3
       0.239 -    0.319: 2
       0.319 -    0.399: 5
  Chirality restraints: 603
  Sorted by residual:
  chirality pdb=" C1  NAG C 304 "
            pdb=" ND2 ASN C 183 "
            pdb=" C2  NAG C 304 "
            pdb=" O5  NAG C 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.00   -0.40 2.00e-01 2.50e+01 3.97e+00
  chirality pdb=" C1  NAG B 304 "
            pdb=" ND2 ASN B 183 "
            pdb=" C2  NAG B 304 "
            pdb=" O5  NAG B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.00   -0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" C1  NAG A 304 "
            pdb=" ND2 ASN A 183 "
            pdb=" C2  NAG A 304 "
            pdb=" O5  NAG A 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.89e+00
  ... (remaining 600 not shown)

  Planarity restraints: 582
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 199 "    0.056 5.00e-02 4.00e+02   8.53e-02 1.16e+01
        pdb=" N   PRO C 200 "   -0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO C 200 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO C 200 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 145 "    0.026 2.00e-02 2.50e+03   2.41e-02 7.28e+00
        pdb=" CG  ASN B 145 "   -0.032 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 145 "    0.004 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 145 "   -0.024 2.00e-02 2.50e+03
        pdb=" C1  NAG B 302 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 199 "    0.040 5.00e-02 4.00e+02   6.10e-02 5.95e+00
        pdb=" N   PRO B 200 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO B 200 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 200 "    0.034 5.00e-02 4.00e+02
  ... (remaining 579 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 99
        2.70 -     3.25: 3219
        3.25 -     3.80: 5135
        3.80 -     4.35: 6307
        4.35 -     4.90: 11312
  Nonbonded interactions: 26072
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 231 "
            pdb=" OG1 THR C 234 "
     model   vdw
     2.152 2.440
  nonbonded pdb=" OD2 ASP A 196 "
            pdb=" OG1 THR A 198 "
     model   vdw
     2.193 2.440
  nonbonded pdb=" NZ  LYS B 129 "
            pdb=" OD2 ASP B 136 "
     model   vdw
     2.201 2.520
  nonbonded pdb=" OD1 ASP B 212 "
            pdb=" OG1 THR B 215 "
     model   vdw
     2.214 2.440
  nonbonded pdb=" NE2 GLN C 249 "
            pdb=" OD2 ASP C 252 "
     model   vdw
     2.225 2.520
  ... (remaining 26067 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  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:          6.610
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     14.150
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3031
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      :  0.005   0.083   3480  Z= 0.332
  Angle     :  0.722   5.489   4731  Z= 0.382
  Chirality :  0.066   0.399    603
  Planarity :  0.006   0.085    570
  Dihedral  : 18.016 124.235   1458
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -4.08 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 239 
   PHE   0.005   0.001   PHE A 237 
   TYR   0.022   0.002   TYR B 250 
   ARG   0.001   0.000   ARG B 247 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1560
  time to fit residues: 19.1989
Evaluate side-chains
  64 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.342 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.4789
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 18 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 249 GLN
B 249 GLN
C 155 ASN
C 170 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5975
moved from start:          1.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060   3480  Z= 0.433
  Angle     :  1.159  11.944   4731  Z= 0.563
  Chirality :  0.086   0.734    603
  Planarity :  0.007   0.064    570
  Dihedral  : 13.189  59.871    699
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.53 %
    Favored  : 86.47 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 17.72 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -4.17 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.17 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS C 222 
   PHE   0.013   0.002   PHE C 213 
   TYR   0.033   0.003   TYR A 197 
   ARG   0.002   0.001   ARG B 140 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 9
  residues processed: 155
  average time/residue: 0.1364
  time to fit residues: 25.9555
Evaluate side-chains
  129 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.419 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0316
  time to fit residues: 1.0140
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   chunk 28 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0470
   overall best weight:    2.6084

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

Flipped N/Q/H residues before XYZ refinement:
** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 GLN
C 170 GLN
C 249 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6790
moved from start:          1.4521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   3480  Z= 0.317
  Angle     :  0.895   8.142   4731  Z= 0.447
  Chirality :  0.070   0.425    603
  Planarity :  0.005   0.051    570
  Dihedral  : 10.393  56.831    699
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.53 %
    Favored  : 86.47 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 21.16 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -4.36 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 239 
   PHE   0.018   0.002   PHE B 171 
   TYR   0.021   0.002   TYR A 248 
   ARG   0.006   0.001   ARG C 140 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 10
  residues processed: 150
  average time/residue: 0.1472
  time to fit residues: 26.6646
Evaluate side-chains
  137 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.385 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0364
  time to fit residues: 1.1751
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          1.6996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3480  Z= 0.280
  Angle     :  0.799   7.704   4731  Z= 0.415
  Chirality :  0.069   0.507    603
  Planarity :  0.006   0.073    570
  Dihedral  :  9.113  51.370    699
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.03 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 21.16 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -4.21 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS C 222 
   PHE   0.018   0.002   PHE B 171 
   TYR   0.020   0.002   TYR B 250 
   ARG   0.005   0.001   ARG A 140 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 10
  residues processed: 140
  average time/residue: 0.1604
  time to fit residues: 26.8219
Evaluate side-chains
  129 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.419 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0368
  time to fit residues: 1.1484
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 9 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    1.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          1.8135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3480  Z= 0.231
  Angle     :  0.730   9.555   4731  Z= 0.383
  Chirality :  0.067   0.459    603
  Planarity :  0.006   0.075    570
  Dihedral  :  8.705  51.451    699
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 23.02 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -4.04 (0.35), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS C 239 
   PHE   0.009   0.002   PHE A 171 
   TYR   0.023   0.002   TYR A 143 
   ARG   0.005   0.001   ARG A 180 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 9
  residues processed: 125
  average time/residue: 0.1675
  time to fit residues: 25.0951
Evaluate side-chains
  124 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.414 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0416
  time to fit residues: 1.1980
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 3 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
C 170 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          1.9723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3480  Z= 0.293
  Angle     :  0.784  10.255   4731  Z= 0.414
  Chirality :  0.068   0.417    603
  Planarity :  0.007   0.080    570
  Dihedral  :  9.174  53.705    699
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 17.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.28 %
    Favored  : 86.72 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 26.72 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -4.07 (0.35), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.09 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS C 239 
   PHE   0.022   0.003   PHE B 213 
   TYR   0.024   0.002   TYR A 143 
   ARG   0.005   0.001   ARG A 180 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 117
  average time/residue: 0.1798
  time to fit residues: 24.8727
Evaluate side-chains
  106 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.414 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0326
  time to fit residues: 0.6484
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 138 GLN
C 239 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          2.0365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3480  Z= 0.269
  Angle     :  0.793   9.089   4731  Z= 0.403
  Chirality :  0.066   0.435    603
  Planarity :  0.007   0.081    570
  Dihedral  :  8.857  54.399    699
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 17.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.03 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 31.48 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -3.98 (0.35), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS C 239 
   PHE   0.014   0.002   PHE B 171 
   TYR   0.024   0.002   TYR A 143 
   ARG   0.003   0.001   ARG A 140 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 114
  average time/residue: 0.1823
  time to fit residues: 24.4417
Evaluate side-chains
  105 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.363 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0366
  time to fit residues: 0.7795
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0170
   chunk 15 optimal weight:    4.9990
   chunk 27 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    3.4026

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

Flipped N/Q/H residues before XYZ refinement:
** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 223 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          2.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3480  Z= 0.346
  Angle     :  0.834   8.128   4731  Z= 0.433
  Chirality :  0.069   0.450    603
  Planarity :  0.007   0.083    570
  Dihedral  :  9.091  59.552    699
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 18.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.04 %
    Favored  : 85.96 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 30.69 %
    Favored  : 66.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -4.04 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.001   HIS C 222 
   PHE   0.014   0.002   PHE B 213 
   TYR   0.020   0.002   TYR A 248 
   ARG   0.004   0.001   ARG C 140 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 6
  residues processed: 114
  average time/residue: 0.1795
  time to fit residues: 24.1581
Evaluate side-chains
  104 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.360 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0324
  time to fit residues: 0.8192
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 17 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   overall best weight:    4.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          2.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   3480  Z= 0.436
  Angle     :  0.880   7.995   4731  Z= 0.454
  Chirality :  0.071   0.483    603
  Planarity :  0.007   0.081    570
  Dihedral  :  9.379  58.161    699
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 20.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.78 %
    Favored  : 86.22 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 29.10 %
    Favored  : 68.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -4.14 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.15 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 239 
   PHE   0.016   0.003   PHE B 171 
   TYR   0.020   0.002   TYR A 143 
   ARG   0.004   0.001   ARG B 247 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 7
  residues processed: 100
  average time/residue: 0.1868
  time to fit residues: 21.8892
Evaluate side-chains
  100 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.353 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0343
  time to fit residues: 0.8826
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 18 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 9 optimal weight:    8.9990
   chunk 28 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 168 GLN
** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          2.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   3480  Z= 0.377
  Angle     :  0.867   8.252   4731  Z= 0.448
  Chirality :  0.069   0.460    603
  Planarity :  0.007   0.079    570
  Dihedral  :  9.268  54.509    699
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 19.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.28 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 29.89 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -4.22 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS B 239 
   PHE   0.015   0.002   PHE B 171 
   TYR   0.022   0.002   TYR A 143 
   ARG   0.004   0.001   ARG B 247 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 101
  average time/residue: 0.1886
  time to fit residues: 22.5212
Evaluate side-chains
  95 residues out of total 378 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.421 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0377
  time to fit residues: 0.6417
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 26 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 23 optimal weight:    0.5980
   chunk 15 optimal weight:    8.9990
   overall best weight:    2.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.132473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.120120 restraints weight = 6180.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.4261 rms_B_bonded: 2.89
r_work: 0.4168 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          2.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3480  Z= 0.259
  Angle     :  0.804   8.445   4731  Z= 0.412
  Chirality :  0.066   0.421    603
  Planarity :  0.007   0.074    570
  Dihedral  :  8.950  53.369    699
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 31.22 %
    Favored  : 68.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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: -4.08 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 239 
   PHE   0.012   0.002   PHE B 171 
   TYR   0.020   0.002   TYR A 143 
   ARG   0.004   0.001   ARG B 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1278.33 seconds
wall clock time: 24 minutes 2.19 seconds (1442.19 seconds total)