Starting phenix.real_space_refine
on Tue Nov 14 16:42:45 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un6_26614/11_2023/7un6_26614.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un6_26614/11_2023/7un6_26614.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un6_26614/11_2023/7un6_26614.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un6_26614/11_2023/7un6_26614.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un6_26614/11_2023/7un6_26614.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un6_26614/11_2023/7un6_26614.pdb"
  }
  resolution = 3.3
  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=  -0.002 sd=   0.068
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      41      5.16       5
     C    5808      2.51       5
     N    1533      2.21       5
     O    1660      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP   64": "OD1" <-> "OD2"
    Residue "A TYR  200": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  202": "OD1" <-> "OD2"
    Residue "A GLU  583": "OE1" <-> "OE2"
    Residue "A PHE  584": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  622": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  691": "OE1" <-> "OE2"
    Residue "A GLU  933": "OE1" <-> "OE2"
    Residue "A TYR  997": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1092": "OE1" <-> "OE2"
    Residue "A TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1123": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1265": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1282": "OE1" <-> "OE2"
    Residue "B TYR  223": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  224": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  324": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  224": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  324": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib"
  Total number of atoms: 9042
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 648, 5186
          Classifications: {'peptide': 648}
          Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 610}
          Chain breaks: 8
    Chain: "B"
      Number of atoms: 1965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1965
          Classifications: {'peptide': 240}
          Link IDs: {'PTRANS': 13, 'TRANS': 226}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1891
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1891
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 11, 'TRANS': 218}
          Chain breaks: 2
  Time building chain proxies: 5.38, per 1000 atoms: 0.60
  Number of scatterers: 9042
  At special positions: 0
  Unit cell: (90.75, 131.175, 135.3, 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      41     16.00
     O    1660      8.00
     N    1533      7.00
     C    5808      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        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
  Time building additional restraints: 3.45
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2110

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      31.8% alpha, 27.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 190 through 192
      No H-bonds generated for 'chain 'A' and resid 190 through 192'
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 271 through 275
      removed outlier: 4.091A  pdb=" N   SER A 275 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 334
      removed outlier: 4.179A  pdb=" N   GLY A 334 " --> pdb=" O   GLN A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 343
    Processing helix  chain 'A' and resid 703 through 705
      No H-bonds generated for 'chain 'A' and resid 703 through 705'
    Processing helix  chain 'A' and resid 950 through 968
    Processing helix  chain 'A' and resid 1060 through 1071
    Processing helix  chain 'A' and resid 1083 through 1088
    Processing helix  chain 'A' and resid 1090 through 1118
      removed outlier: 3.535A  pdb=" N   ARG A1117 " --> pdb=" O   THR A1113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1123 through 1146
      removed outlier: 3.751A  pdb=" N   ARG A1128 " --> pdb=" O   GLU A1124 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   THR A1133 " --> pdb=" O   GLN A1129 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   TRP A1136 " --> pdb=" O   SER A1132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1262 through 1283
    Processing helix  chain 'B' and resid 74 through 122
      Proline residue:  B 112  - end of helix
    Processing helix  chain 'B' and resid 169 through 178
    Processing helix  chain 'B' and resid 178 through 183
    Processing helix  chain 'B' and resid 189 through 194
    Processing helix  chain 'B' and resid 243 through 247
    Processing helix  chain 'B' and resid 296 through 301
    Processing helix  chain 'B' and resid 313 through 333
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.655A  pdb=" N   TYR B 341 " --> pdb=" O   ARG B 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 123
      Proline residue:  C 112  - end of helix
    Processing helix  chain 'C' and resid 169 through 177
    Processing helix  chain 'C' and resid 178 through 183
    Processing helix  chain 'C' and resid 189 through 194
    Processing helix  chain 'C' and resid 243 through 247
    Processing helix  chain 'C' and resid 296 through 302
    Processing helix  chain 'C' and resid 316 through 333
    Processing helix  chain 'C' and resid 337 through 343
    Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134
      removed outlier: 6.272A  pdb=" N   LEU A  65 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 188
      removed outlier: 6.668A  pdb=" N   ILE A 183 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   LEU A 177 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   TYR A 185 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   VAL A 175 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ASP A 556 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   VAL A 169 " --> pdb=" O   SER A 554 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   SER A 554 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ILE A 171 " --> pdb=" O   MET A 552 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   MET A 552 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   CYS A 173 " --> pdb=" O   THR A 550 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   THR A 550 " --> pdb=" O   CYS A 173 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   VAL A 175 " --> pdb=" O   VAL A 548 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL A 548 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   LEU A 177 " --> pdb=" O   VAL A 546 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   VAL A 546 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   VAL A 557 " --> pdb=" O   CYS A 566 " (cutoff:3.500A)
      removed outlier: 5.637A  pdb=" N   CYS A 566 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   TRP A 559 " --> pdb=" O   VAL A 564 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   VAL A 564 " --> pdb=" O   TRP A 559 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 356
      removed outlier: 6.662A  pdb=" N   VAL A 546 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   LEU A 177 " --> pdb=" O   VAL A 546 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL A 548 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   VAL A 175 " --> pdb=" O   VAL A 548 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   THR A 550 " --> pdb=" O   CYS A 173 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   CYS A 173 " --> pdb=" O   THR A 550 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   MET A 552 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ILE A 171 " --> pdb=" O   MET A 552 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   SER A 554 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   VAL A 169 " --> pdb=" O   SER A 554 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ASP A 556 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 269
      removed outlier: 6.753A  pdb=" N   GLU A 297 " --> pdb=" O   LYS A 223 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   LYS A 223 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   VAL A 299 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ILE A 221 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   VAL A 301 " --> pdb=" O   GLN A 219 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   GLN A 219 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP A 215 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 280
      removed outlier: 5.963A  pdb=" N   TRP A 278 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   SER A 231 " --> pdb=" O   TRP A 278 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP A 215 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   GLN A 219 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   VAL A 301 " --> pdb=" O   GLN A 219 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ILE A 221 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   VAL A 299 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   LYS A 223 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   GLU A 297 " --> pdb=" O   LYS A 223 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 291 through 306
    current: chain 'A' and resid 337 through 338
    Processing sheet with id=AA6, first strand: chain 'A' and resid 631 through 635
      removed outlier: 6.530A  pdb=" N   TRP A 621 " --> pdb=" O   ILE A 634 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 631 through 635
      removed outlier: 6.530A  pdb=" N   TRP A 621 " --> pdb=" O   ILE A 634 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   THR A 616 " --> pdb=" O   ASP A 611 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   SER A 609 " --> pdb=" O   MET A 618 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   LYS A 620 " --> pdb=" O   VAL A 607 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   VAL A 607 " --> pdb=" O   LYS A 620 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   PHE A 622 " --> pdb=" O   GLY A 605 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   GLY A 605 " --> pdb=" O   PHE A 622 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   LEU A 624 " --> pdb=" O   VAL A 603 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   VAL A 603 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
      removed outlier: 8.557A  pdb=" N   VAL A 603 " --> pdb=" O   ASP A 592 " (cutoff:3.500A)
      removed outlier: 5.236A  pdb=" N   ASP A 592 " --> pdb=" O   VAL A 603 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 680 through 681
    Processing sheet with id=AA9, first strand: chain 'A' and resid 931 through 932
      removed outlier: 3.873A  pdb=" N   PHE A 978 " --> pdb=" O   LEU A 984 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   LEU A 984 " --> pdb=" O   PHE A 978 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   GLY A 991 " --> pdb=" O   GLY A1000 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   GLY A1000 " --> pdb=" O   GLY A 991 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 196 through 203
      removed outlier: 4.035A  pdb=" N   LEU B 214 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   LYS B 231 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ARG B 234 " --> pdb=" O   GLY B 254 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLY B 254 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   ARG B 236 " --> pdb=" O   ILE B 252 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ILE B 252 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 270 through 278
    Processing sheet with id=AB3, first strand: chain 'C' and resid 199 through 203
    Processing sheet with id=AB4, first strand: chain 'C' and resid 233 through 235
      removed outlier: 5.790A  pdb=" N   ARG C 234 " --> pdb=" O   MET C 253 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 270 through 278

    353 hydrogen bonds defined for protein.
    990 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: 2.73

  Time building geometry restraints manager: 3.78 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: 2928
        1.34 -     1.46: 1983
        1.46 -     1.58: 4281
        1.58 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 9253
  Sorted by residual:
  bond pdb=" C   PHE A 584 "
       pdb=" N   CYS A 585 "
    ideal  model  delta    sigma   weight residual
    1.329  1.248  0.081 1.86e-02 2.89e+03 1.87e+01
  bond pdb=" CG  LEU C  81 "
       pdb=" CD2 LEU C  81 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.30e+00
  bond pdb=" CB  VAL C 201 "
       pdb=" CG2 VAL C 201 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.99e-01
  bond pdb=" CB  GLU A1081 "
       pdb=" CG  GLU A1081 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.93e-01
  bond pdb=" CB  ILE B 192 "
       pdb=" CG1 ILE B 192 "
    ideal  model  delta    sigma   weight residual
    1.530  1.512  0.018 2.00e-02 2.50e+03 8.33e-01
  ... (remaining 9248 not shown)

  Histogram of bond angle deviations from ideal:
       97.58 -   104.86: 179
      104.86 -   112.14: 4562
      112.14 -   119.42: 3105
      119.42 -   126.70: 4524
      126.70 -   133.98: 140
  Bond angle restraints: 12510
  Sorted by residual:
  angle pdb=" N   GLU A 691 "
        pdb=" CA  GLU A 691 "
        pdb=" C   GLU A 691 "
      ideal   model   delta    sigma   weight residual
     111.07  115.58   -4.51 1.07e+00 8.73e-01 1.78e+01
  angle pdb=" CA  GLU A1081 "
        pdb=" CB  GLU A1081 "
        pdb=" CG  GLU A1081 "
      ideal   model   delta    sigma   weight residual
     114.10  121.36   -7.26 2.00e+00 2.50e-01 1.32e+01
  angle pdb=" N   GLN B 111 "
        pdb=" CA  GLN B 111 "
        pdb=" C   GLN B 111 "
      ideal   model   delta    sigma   weight residual
     113.77  109.79    3.98 1.32e+00 5.74e-01 9.09e+00
  angle pdb=" N   VAL A 692 "
        pdb=" CA  VAL A 692 "
        pdb=" C   VAL A 692 "
      ideal   model   delta    sigma   weight residual
     107.75  111.45   -3.70 1.46e+00 4.69e-01 6.41e+00
  angle pdb=" C   ILE A 973 "
        pdb=" N   MET A 974 "
        pdb=" CA  MET A 974 "
      ideal   model   delta    sigma   weight residual
     121.80  117.67    4.13 1.71e+00 3.42e-01 5.82e+00
  ... (remaining 12505 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 5060
       17.81 -    35.62: 413
       35.62 -    53.43: 61
       53.43 -    71.24: 17
       71.24 -    89.05: 14
  Dihedral angle restraints: 5565
    sinusoidal: 2315
      harmonic: 3250
  Sorted by residual:
  dihedral pdb=" CA  GLU A 691 "
           pdb=" C   GLU A 691 "
           pdb=" N   VAL A 692 "
           pdb=" CA  VAL A 692 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.46  -27.54     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  ASN C 221 "
           pdb=" C   ASN C 221 "
           pdb=" N   GLU C 222 "
           pdb=" CA  GLU C 222 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.04   21.96     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  ILE A 973 "
           pdb=" C   ILE A 973 "
           pdb=" N   MET A 974 "
           pdb=" CA  MET A 974 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.11   21.89     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 5562 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 979
       0.039 -    0.078: 263
       0.078 -    0.117: 103
       0.117 -    0.156: 24
       0.156 -    0.195: 1
  Chirality restraints: 1370
  Sorted by residual:
  chirality pdb=" CB  ILE B 192 "
            pdb=" CA  ILE B 192 "
            pdb=" CG1 ILE B 192 "
            pdb=" CG2 ILE B 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.20 2.00e-01 2.50e+01 9.54e-01
  chirality pdb=" CA  PHE C 216 "
            pdb=" N   PHE C 216 "
            pdb=" C   PHE C 216 "
            pdb=" CB  PHE C 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.05e-01
  chirality pdb=" CA  ILE B 199 "
            pdb=" N   ILE B 199 "
            pdb=" C   ILE B 199 "
            pdb=" CB  ILE B 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.53e-01
  ... (remaining 1367 not shown)

  Planarity restraints: 1608
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 154 "   -0.177 9.50e-02 1.11e+02   7.93e-02 4.03e+00
        pdb=" NE  ARG A 154 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 154 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 154 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 154 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 111 "   -0.024 5.00e-02 4.00e+02   3.60e-02 2.07e+00
        pdb=" N   PRO B 112 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 112 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 112 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 622 "    0.009 2.00e-02 2.50e+03   1.06e-02 1.97e+00
        pdb=" CG  PHE A 622 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 622 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 622 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 622 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 622 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 622 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1605 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 50
        2.48 -     3.09: 6799
        3.09 -     3.69: 13564
        3.69 -     4.30: 19819
        4.30 -     4.90: 32624
  Nonbonded interactions: 72856
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 233 "
            pdb=" OD1 ASP C 323 "
     model   vdw
     1.879 2.440
  nonbonded pdb=" OG  SER A 287 "
            pdb=" OD2 ASP C 248 "
     model   vdw
     1.955 2.440
  nonbonded pdb=" OH  TYR A 997 "
            pdb=" O   LEU A1029 "
     model   vdw
     1.985 2.440
  nonbonded pdb=" OH  TYR A  70 "
            pdb=" OE1 GLU A 129 "
     model   vdw
     2.082 2.440
  nonbonded pdb=" OH  TYR B 233 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.126 2.440
  ... (remaining 72851 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 'B' and (resid 73 through 126 or resid 166 through 306 or resid 315 throu \ 
gh 349))
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          8.590
  Check model and map are aligned:         0.140
  Set scattering table:                    0.100
  Process input model:                     28.710
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.040
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5485
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      :  0.004   0.081   9253  Z= 0.243
  Angle     :  0.600   7.257  12510  Z= 0.331
  Chirality :  0.044   0.195   1370
  Planarity :  0.004   0.079   1608
  Dihedral  : 13.875  89.046   3455
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.89 (0.25), residues: 1090
  helix:  0.66 (0.30), residues: 293
  sheet: -1.50 (0.32), residues: 218
  loop : -0.80 (0.26), residues: 579

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.2412
  time to fit residues: 60.1915
Evaluate side-chains
  110 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.018 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4538
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 84 optimal weight:   10.0000
   chunk 46 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 56 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 87 optimal weight:    0.6980
   chunk 33 optimal weight:    8.9990
   chunk 52 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  75 HIS
A 346 GLN
A1101 ASN
B 111 GLN
** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 100 HIS
C 111 GLN
C 221 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5625
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9253  Z= 0.271
  Angle     :  0.655   7.432  12510  Z= 0.339
  Chirality :  0.046   0.185   1370
  Planarity :  0.005   0.068   1608
  Dihedral  :  5.113  27.661   1201
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.93 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.48 (0.25), residues: 1090
  helix:  0.92 (0.30), residues: 286
  sheet: -1.29 (0.32), residues: 219
  loop : -0.47 (0.27), residues: 585

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 8
  residues processed: 123
  average time/residue: 0.1666
  time to fit residues: 31.3803
Evaluate side-chains
  108 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 1.066 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0791
  time to fit residues: 2.5409
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 83 optimal weight:    0.0570
   chunk 68 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 109 optimal weight:    0.7980
   chunk 89 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0270
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 ASN
C 111 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5603
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9253  Z= 0.186
  Angle     :  0.565   7.034  12510  Z= 0.292
  Chirality :  0.044   0.167   1370
  Planarity :  0.004   0.063   1608
  Dihedral  :  4.811  22.685   1201
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.62 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.19 (0.25), residues: 1090
  helix:  1.03 (0.30), residues: 287
  sheet: -1.13 (0.32), residues: 207
  loop : -0.23 (0.26), residues: 596

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 7
  residues processed: 122
  average time/residue: 0.1676
  time to fit residues: 31.3722
Evaluate side-chains
  111 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 1.051 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0908
  time to fit residues: 2.7263
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 52 optimal weight:   20.0000
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 67 optimal weight:    0.0870
   chunk 101 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.8160

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5664
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9253  Z= 0.236
  Angle     :  0.583   7.142  12510  Z= 0.298
  Chirality :  0.044   0.186   1370
  Planarity :  0.004   0.056   1608
  Dihedral  :  4.786  22.207   1201
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.59 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.24 (0.25), residues: 1090
  helix:  0.87 (0.30), residues: 295
  sheet: -0.96 (0.31), residues: 219
  loop : -0.27 (0.27), residues: 576

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 10
  residues processed: 121
  average time/residue: 0.1671
  time to fit residues: 30.8303
Evaluate side-chains
  112 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 1.009 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0873
  time to fit residues: 3.0927
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 79 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 36 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 170 ASN
B 188 HIS
C 111 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5733
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   9253  Z= 0.320
  Angle     :  0.626   8.521  12510  Z= 0.321
  Chirality :  0.046   0.158   1370
  Planarity :  0.004   0.047   1608
  Dihedral  :  5.007  22.771   1201
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.68 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.31 (0.25), residues: 1090
  helix:  0.76 (0.30), residues: 288
  sheet: -1.10 (0.33), residues: 205
  loop : -0.25 (0.26), residues: 597

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
  outliers start: 21
  outliers final: 13
  residues processed: 125
  average time/residue: 0.1743
  time to fit residues: 32.8211
Evaluate side-chains
  116 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.953 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.1062
  time to fit residues: 3.7802
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 49 optimal weight:   20.0000
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 56 optimal weight:    8.9990
   chunk 103 optimal weight:    5.9990
   chunk 12 optimal weight:    0.4980
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
A 155 HIS
A 170 ASN
C 111 GLN
C 221 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5740
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9253  Z= 0.293
  Angle     :  0.607   7.276  12510  Z= 0.312
  Chirality :  0.046   0.178   1370
  Planarity :  0.004   0.049   1608
  Dihedral  :  4.982  23.613   1201
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.58 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.34 (0.25), residues: 1090
  helix:  0.71 (0.30), residues: 288
  sheet: -0.98 (0.33), residues: 205
  loop : -0.32 (0.26), residues: 597

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 9
  residues processed: 119
  average time/residue: 0.1765
  time to fit residues: 31.6445
Evaluate side-chains
  109 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.953 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.1945
  time to fit residues: 3.9978
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 78 optimal weight:    0.1980
   chunk 60 optimal weight:    9.9990
   chunk 90 optimal weight:    0.6980
   chunk 59 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0870
   chunk 42 optimal weight:    8.9990
   chunk 63 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
A 170 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5673
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9253  Z= 0.187
  Angle     :  0.574   8.575  12510  Z= 0.288
  Chirality :  0.044   0.228   1370
  Planarity :  0.004   0.045   1608
  Dihedral  :  4.769  23.268   1201
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 16.07 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.14 (0.25), residues: 1090
  helix:  0.70 (0.30), residues: 295
  sheet: -0.80 (0.33), residues: 205
  loop : -0.12 (0.27), residues: 590

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.969 
Fit side-chains
  outliers start: 12
  outliers final: 9
  residues processed: 113
  average time/residue: 0.1722
  time to fit residues: 29.3708
Evaluate side-chains
  111 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.953 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0848
  time to fit residues: 2.7906
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    0.0670
   chunk 20 optimal weight:    0.0270
   chunk 68 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 102 optimal weight:    0.5980
   chunk 93 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.4176

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
C 328 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5653
moved from start:          0.3797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9253  Z= 0.174
  Angle     :  0.560   7.896  12510  Z= 0.284
  Chirality :  0.044   0.173   1370
  Planarity :  0.004   0.045   1608
  Dihedral  :  4.702  23.208   1201
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 16.96 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.06 (0.25), residues: 1090
  helix:  0.77 (0.30), residues: 295
  sheet: -0.74 (0.34), residues: 206
  loop : -0.08 (0.27), residues: 589

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 5
  residues processed: 113
  average time/residue: 0.1705
  time to fit residues: 29.3850
Evaluate side-chains
  105 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.937 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0918
  time to fit residues: 2.2625
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 102 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0670
   chunk 30 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    1.7724

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
A 170 ASN
A 193 GLN
C 122 ASN
C 221 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5798
moved from start:          0.4059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   9253  Z= 0.415
  Angle     :  0.695   7.410  12510  Z= 0.358
  Chirality :  0.048   0.199   1370
  Planarity :  0.005   0.045   1608
  Dihedral  :  5.260  23.391   1201
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 17.76 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.53 (0.25), residues: 1090
  helix:  0.38 (0.30), residues: 294
  sheet: -1.08 (0.34), residues: 205
  loop : -0.34 (0.26), residues: 591

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 2
  residues processed: 108
  average time/residue: 0.1869
  time to fit residues: 31.0071
Evaluate side-chains
  101 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.977 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0826
  time to fit residues: 1.7035
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   chunk 110 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 53 optimal weight:   10.0000
   chunk 69 optimal weight:    0.0980
   chunk 93 optimal weight:    0.9980
   chunk 26 optimal weight:    0.4980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
A 170 ASN
A 193 GLN
** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 328 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5687
moved from start:          0.4103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9253  Z= 0.195
  Angle     :  0.594   8.703  12510  Z= 0.300
  Chirality :  0.044   0.219   1370
  Planarity :  0.004   0.046   1608
  Dihedral  :  4.938  25.320   1201
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 18.25 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.26 (0.26), residues: 1090
  helix:  0.60 (0.30), residues: 294
  sheet: -0.78 (0.34), residues: 210
  loop : -0.22 (0.27), residues: 586

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 4
  residues processed: 112
  average time/residue: 0.1614
  time to fit residues: 27.7724
Evaluate side-chains
  109 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.892 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.2203
  time to fit residues: 2.7337
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 90 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0070
   chunk 16 optimal weight:    0.4980
   chunk 77 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0020
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.3406

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

Flipped N/Q/H residues before XYZ refinement:
A  83 HIS
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5024 r_free = 0.5024 target = 0.278172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.230402 restraints weight = 8713.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.4630 rms_B_bonded: 3.27
r_work: 0.4240 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6735
moved from start:          0.4231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9253  Z= 0.166
  Angle     :  0.572   9.598  12510  Z= 0.288
  Chirality :  0.044   0.205   1370
  Planarity :  0.004   0.046   1608
  Dihedral  :  4.748  25.876   1201
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 18.15 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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: -0.07 (0.26), residues: 1090
  helix:  0.77 (0.30), residues: 295
  sheet: -0.59 (0.34), residues: 213
  loop : -0.14 (0.27), residues: 582
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2108.24 seconds
wall clock time: 38 minutes 59.88 seconds (2339.88 seconds total)