Starting phenix.real_space_refine
on Tue Feb 13 18:12:01 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8t_15921/02_2024/8b8t_15921_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8t_15921/02_2024/8b8t_15921.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8t_15921/02_2024/8b8t_15921.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8t_15921/02_2024/8b8t_15921.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8t_15921/02_2024/8b8t_15921_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8t_15921/02_2024/8b8t_15921_neut.pdb"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      49      5.16       5
     C    4520      2.51       5
     N    1202      2.21       5
     O    1409      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  387": "NH1" <-> "NH2"
    Residue "A ARG  440": "NH1" <-> "NH2"
    Residue "E ARG    5": "NH1" <-> "NH2"
    Residue "E ARG   53": "NH1" <-> "NH2"
    Residue "E ARG   61": "NH1" <-> "NH2"
    Residue "E ARG   64": "NH1" <-> "NH2"
    Residue "E ARG   91": "NH1" <-> "NH2"
    Residue "E ARG  146": "NH1" <-> "NH2"
    Residue "E ARG  149": "NH1" <-> "NH2"
    Residue "E ARG  210": "NH1" <-> "NH2"
    Residue "F ARG    5": "NH1" <-> "NH2"
    Residue "F ARG   53": "NH1" <-> "NH2"
    Residue "F ARG   61": "NH1" <-> "NH2"
    Residue "F ARG   64": "NH1" <-> "NH2"
    Residue "F ARG   91": "NH1" <-> "NH2"
    Residue "F ARG  146": "NH1" <-> "NH2"
    Residue "F ARG  149": "NH1" <-> "NH2"
    Residue "F ARG  210": "NH1" <-> "NH2"
    Residue "G ARG    5": "NH1" <-> "NH2"
    Residue "G ARG   53": "NH1" <-> "NH2"
    Residue "G ARG   61": "NH1" <-> "NH2"
    Residue "G ARG   64": "NH1" <-> "NH2"
    Residue "G ARG   91": "NH1" <-> "NH2"
    Residue "G ARG  146": "NH1" <-> "NH2"
    Residue "G ARG  149": "NH1" <-> "NH2"
    Residue "G ARG  210": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 7180
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1510
          Classifications: {'peptide': 241}
          Incomplete info: {'truncation_to_alanine': 91}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 223}
          Chain breaks: 4
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 351
          Unresolved non-hydrogen angles: 432
          Unresolved non-hydrogen dihedrals: 292
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 14}
          Unresolved non-hydrogen planarities: 191
    Chain: "E"
      Number of atoms: 1898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1898
          Classifications: {'peptide': 251}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 7, 'TRANS': 243}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "F"
      Number of atoms: 1887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 1887
          Classifications: {'peptide': 249}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 7, 'TRANS': 241}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "G"
      Number of atoms: 1885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 1885
          Classifications: {'peptide': 248}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 7, 'TRANS': 240}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 14
  Time building chain proxies: 4.32, per 1000 atoms: 0.60
  Number of scatterers: 7180
  At special positions: 0
  Unit cell: (121.632, 98.826, 115.116, 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      49     16.00
     O    1409      8.00
     N    1202      7.00
     C    4520      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: 2.78
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1872

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 7 sheets defined
      32.5% alpha, 28.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 288 through 301
      removed outlier: 4.232A  pdb=" N   VAL A 292 " --> pdb=" O   PRO A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 323
    Processing helix  chain 'A' and resid 326 through 335
    Processing helix  chain 'A' and resid 351 through 363
    Processing helix  chain 'A' and resid 365 through 374
      removed outlier: 3.506A  pdb=" N   ALA A 374 " --> pdb=" O   ARG A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 390
      removed outlier: 3.873A  pdb=" N   VAL A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 412
    Processing helix  chain 'A' and resid 421 through 434
      removed outlier: 3.655A  pdb=" N   ALA A 433 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   CYS A 434 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 448
    Processing helix  chain 'A' and resid 455 through 470
    Processing helix  chain 'A' and resid 488 through 506
    Processing helix  chain 'A' and resid 513 through 523
      Proline residue:  A 518  - end of helix
    Processing helix  chain 'E' and resid 9 through 20
      removed outlier: 4.139A  pdb=" N   LYS E  13 " --> pdb=" O   GLY E   9 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 57
      No H-bonds generated for 'chain 'E' and resid 55 through 57'
    Processing helix  chain 'E' and resid 72 through 81
      removed outlier: 3.878A  pdb=" N   CYS E  81 " --> pdb=" O   LYS E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 141 through 153
      removed outlier: 3.784A  pdb=" N   HIS E 153 " --> pdb=" O   ARG E 149 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 209 through 216
    Processing helix  chain 'E' and resid 217 through 222
      Proline residue:  E 220  - end of helix
      No H-bonds generated for 'chain 'E' and resid 217 through 222'
    Processing helix  chain 'F' and resid 8 through 19
      removed outlier: 3.993A  pdb=" N   LEU F  12 " --> pdb=" O   GLN F   8 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU F  19 " --> pdb=" O   VAL F  15 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 55 through 57
      No H-bonds generated for 'chain 'F' and resid 55 through 57'
    Processing helix  chain 'F' and resid 72 through 80
    Processing helix  chain 'F' and resid 141 through 153
      removed outlier: 3.656A  pdb=" N   SER F 152 " --> pdb=" O   CYS F 148 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   HIS F 153 " --> pdb=" O   ARG F 149 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 209 through 216
    Processing helix  chain 'F' and resid 217 through 222
      Proline residue:  F 220  - end of helix
      No H-bonds generated for 'chain 'F' and resid 217 through 222'
    Processing helix  chain 'G' and resid 8 through 20
      removed outlier: 3.782A  pdb=" N   LEU G  12 " --> pdb=" O   GLN G   8 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 57
      No H-bonds generated for 'chain 'G' and resid 55 through 57'
    Processing helix  chain 'G' and resid 72 through 80
    Processing helix  chain 'G' and resid 141 through 155
      removed outlier: 4.313A  pdb=" N   HIS G 153 " --> pdb=" O   ARG G 149 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ILE G 154 " --> pdb=" O   ASP G 150 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 209 through 217
      removed outlier: 3.785A  pdb=" N   LYS G 217 " --> pdb=" O   ASN G 213 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 218 through 222
    Processing sheet with id=AA1, first strand: chain 'E' and resid 59 through 62
      removed outlier: 3.803A  pdb=" N   THR E  59 " --> pdb=" O   ARG E   5 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL F 167 " --> pdb=" O   LEU F 182 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   SER F 172 " --> pdb=" O   ALA F 157 " (cutoff:3.500A)
      removed outlier: 5.468A  pdb=" N   ALA F 157 " --> pdb=" O   SER F 172 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 67 through 71
      removed outlier: 3.634A  pdb=" N   ALA E  26 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   GLU E  25 " --> pdb=" O   MET E  40 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   MET E  40 " --> pdb=" O   GLU E  25 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   CYS E  27 " --> pdb=" O   GLN E  38 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   GLN E  38 " --> pdb=" O   CYS E  27 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   LYS E 240 " --> pdb=" O   THR E 224 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   THR E 224 " --> pdb=" O   LYS E 240 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   MET E 229 " --> pdb=" O   CYS E 135 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   CYS E 135 " --> pdb=" O   MET E 229 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 204 through 208
      removed outlier: 5.384A  pdb=" N   ALA E 157 " --> pdb=" O   SER E 172 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   SER E 172 " --> pdb=" O   ALA E 157 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ASN E 177 " --> pdb=" O   GLU G 115 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASN E 179 " --> pdb=" O   ASP G 113 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   VAL G 111 " --> pdb=" O   LYS E 181 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 59 through 61
      removed outlier: 3.746A  pdb=" N   THR F  59 " --> pdb=" O   ARG F   5 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   SER G 172 " --> pdb=" O   ALA G 157 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   ALA G 157 " --> pdb=" O   SER G 172 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 25 through 30
      removed outlier: 4.006A  pdb=" N   ALA F  26 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL F  70 " --> pdb=" O   ALA F  26 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 34 through 40
      removed outlier: 3.851A  pdb=" N   LEU F  47 " --> pdb=" O   TYR F 250 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   HIS F 246 " --> pdb=" O   THR F  51 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   GLY F 245 " --> pdb=" O   ILE F 241 " (cutoff:3.500A)
      removed outlier: 5.204A  pdb=" N   LYS F 240 " --> pdb=" O   THR F 224 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   THR F 224 " --> pdb=" O   LYS F 240 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL F 136 " --> pdb=" O   GLU F 198 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 69 through 71
      removed outlier: 6.885A  pdb=" N   GLU G  25 " --> pdb=" O   MET G  40 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   MET G  40 " --> pdb=" O   GLU G  25 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   CYS G  27 " --> pdb=" O   GLN G  38 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   GLN G  38 " --> pdb=" O   CYS G  27 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU G  37 " --> pdb=" O   LEU G  50 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   LYS G 240 " --> pdb=" O   THR G 224 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   THR G 224 " --> pdb=" O   LYS G 240 " (cutoff:3.500A)

    418 hydrogen bonds defined for protein.
    1176 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: 2.43

  Time building geometry restraints manager: 3.01 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2029
        1.33 -     1.46: 1068
        1.46 -     1.58: 4101
        1.58 -     1.70: 0
        1.70 -     1.82: 78
  Bond restraints: 7276
  Sorted by residual:
  bond pdb=" CA  PRO A 471 "
       pdb=" C   PRO A 471 "
    ideal  model  delta    sigma   weight residual
    1.514  1.545 -0.031 5.50e-03 3.31e+04 3.21e+01
  bond pdb=" CA  ILE A 517 "
       pdb=" CB  ILE A 517 "
    ideal  model  delta    sigma   weight residual
    1.539  1.521  0.018 5.40e-03 3.43e+04 1.12e+01
  bond pdb=" CZ  ARG F  91 "
       pdb=" NH2 ARG F  91 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 9.15e+00
  bond pdb=" CZ  ARG A 387 "
       pdb=" NH2 ARG A 387 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 9.08e+00
  bond pdb=" CA  PRO A 395 "
       pdb=" C   PRO A 395 "
    ideal  model  delta    sigma   weight residual
    1.517  1.544 -0.027 9.30e-03 1.16e+04 8.66e+00
  ... (remaining 7271 not shown)

  Histogram of bond angle deviations from ideal:
       97.66 -   105.04: 126
      105.04 -   112.43: 3265
      112.43 -   119.82: 3076
      119.82 -   127.21: 3361
      127.21 -   134.60: 51
  Bond angle restraints: 9879
  Sorted by residual:
  angle pdb=" N   PRO A 478 "
        pdb=" CA  PRO A 478 "
        pdb=" CB  PRO A 478 "
      ideal   model   delta    sigma   weight residual
     103.17  108.99   -5.82 8.90e-01 1.26e+00 4.28e+01
  angle pdb=" CA  PHE G 215 "
        pdb=" CB  PHE G 215 "
        pdb=" CG  PHE G 215 "
      ideal   model   delta    sigma   weight residual
     113.80  119.00   -5.20 1.00e+00 1.00e+00 2.70e+01
  angle pdb=" C   ASP F 243 "
        pdb=" N   MET F 244 "
        pdb=" CA  MET F 244 "
      ideal   model   delta    sigma   weight residual
     120.29  127.48   -7.19 1.42e+00 4.96e-01 2.56e+01
  angle pdb=" CB  HIS E 246 "
        pdb=" CG  HIS E 246 "
        pdb=" CD2 HIS E 246 "
      ideal   model   delta    sigma   weight residual
     131.20  124.76    6.44 1.30e+00 5.92e-01 2.45e+01
  angle pdb=" CA  PHE A 296 "
        pdb=" CB  PHE A 296 "
        pdb=" CG  PHE A 296 "
      ideal   model   delta    sigma   weight residual
     113.80  118.75   -4.95 1.00e+00 1.00e+00 2.45e+01
  ... (remaining 9874 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 4085
       17.88 -    35.76: 273
       35.76 -    53.64: 57
       53.64 -    71.51: 19
       71.51 -    89.39: 8
  Dihedral angle restraints: 4442
    sinusoidal: 1571
      harmonic: 2871
  Sorted by residual:
  dihedral pdb=" C   ASP F 243 "
           pdb=" N   ASP F 243 "
           pdb=" CA  ASP F 243 "
           pdb=" CB  ASP F 243 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.27   13.67     0      2.50e+00 1.60e-01 2.99e+01
  dihedral pdb=" CA  GLY E 155 "
           pdb=" C   GLY E 155 "
           pdb=" N   ASP E 156 "
           pdb=" CA  ASP E 156 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.69  -27.31     0      5.00e+00 4.00e-02 2.98e+01
  dihedral pdb=" C   ASN A 336 "
           pdb=" N   ASN A 336 "
           pdb=" CA  ASN A 336 "
           pdb=" CB  ASN A 336 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.61   12.01     0      2.50e+00 1.60e-01 2.31e+01
  ... (remaining 4439 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 917
       0.099 -    0.198: 251
       0.198 -    0.296: 23
       0.296 -    0.395: 6
       0.395 -    0.494: 2
  Chirality restraints: 1199
  Sorted by residual:
  chirality pdb=" CA  ASP F 243 "
            pdb=" N   ASP F 243 "
            pdb=" C   ASP F 243 "
            pdb=" CB  ASP F 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.10e+00
  chirality pdb=" CA  ASN A 336 "
            pdb=" N   ASN A 336 "
            pdb=" C   ASN A 336 "
            pdb=" CB  ASN A 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.05e+00
  chirality pdb=" CA  THR E 219 "
            pdb=" N   THR E 219 "
            pdb=" C   THR E 219 "
            pdb=" CB  THR E 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.15    0.37 2.00e-01 2.50e+01 3.51e+00
  ... (remaining 1196 not shown)

  Planarity restraints: 1278
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 211 "   -0.114 2.00e-02 2.50e+03   6.11e-02 7.47e+01
        pdb=" CG  TYR F 211 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 211 "    0.058 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 211 "    0.046 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 211 "    0.028 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 211 "    0.037 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 211 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR F 211 "   -0.089 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP F  28 "    0.092 2.00e-02 2.50e+03   4.90e-02 6.00e+01
        pdb=" CG  TRP F  28 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TRP F  28 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP F  28 "   -0.062 2.00e-02 2.50e+03
        pdb=" NE1 TRP F  28 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE2 TRP F  28 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE3 TRP F  28 "   -0.069 2.00e-02 2.50e+03
        pdb=" CZ2 TRP F  28 "    0.047 2.00e-02 2.50e+03
        pdb=" CZ3 TRP F  28 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP F  28 "    0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR G 211 "    0.097 2.00e-02 2.50e+03   5.10e-02 5.20e+01
        pdb=" CG  TYR G 211 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR G 211 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 TYR G 211 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE1 TYR G 211 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR G 211 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR G 211 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR G 211 "    0.073 2.00e-02 2.50e+03
  ... (remaining 1275 not shown)

  Histogram of nonbonded interaction distances:
        2.56 -     3.03: 3614
        3.03 -     3.49: 7395
        3.49 -     3.96: 10389
        3.96 -     4.43: 10957
        4.43 -     4.90: 19369
  Nonbonded interactions: 51724
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP G  41 "
            pdb=" OG  SER G  46 "
     model   vdw
     2.558 2.440
  nonbonded pdb=" O   ASN E  71 "
            pdb=" OG  SER E  74 "
     model   vdw
     2.566 2.440
  nonbonded pdb=" O   LEU A 331 "
            pdb=" OG  SER A 334 "
     model   vdw
     2.570 2.440
  nonbonded pdb=" O   THR G 216 "
            pdb=" OG1 THR G 219 "
     model   vdw
     2.579 2.440
  nonbonded pdb=" OG  SER F 134 "
            pdb=" OE2 GLU F 201 "
     model   vdw
     2.589 2.440
  ... (remaining 51719 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 'E' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 13 through 28 or (resid 29 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 30 through 51 or (resid 52 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 53 through 107 or re \ 
sid 109 through 115 or (resid 116 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 117 through 127 or (resid 128 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 129 through 163 or (resid 164 through 165 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 166 through 180  \ 
or (resid 181 and (name N or name CA or name C or name O or name CB )) or resid  \ 
182 through 185 or resid 193 through 228 or (resid 229 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 230 through 235 or (resid 236 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 237 or (resid 238 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 239 or (resid 240 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 241 through 255 \ 
))
  selection = (chain 'F' and (resid 1 through 6 or (resid 7 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 8 through 11 or (resid 12 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 13 through 28 or (resid 29 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 30 through 39 or (resid \ 
 40 and (name N or name CA or name C or name O or name CB )) or resid 41 through \ 
 103 or (resid 104 through 105 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 106 through 110 or (resid 111 through 112 and (name N or name C \ 
A or name C or name O or name CB )) or resid 113 through 120 or (resid 121 throu \ 
gh 123 and (name N or name CA or name C or name O or name CB )) or resid 124 thr \ 
ough 151 or (resid 152 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 153 through 160 or (resid 161 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 162 through 163 or (resid 164 through 165 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 166 through 167 or (resid 1 \ 
68 and (name N or name CA or name C or name O or name CB )) or resid 169 through \ 
 185 or resid 193 through 255))
  selection = (chain 'G' and (resid 1 through 6 or (resid 7 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 8 through 39 or (resid 40 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 41 through 51 or (resid 52 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 53 through 106 or (resi \ 
d 107 and (name N or name CA or name C or name O or name CB )) or resid 109 thro \ 
ugh 110 or (resid 111 through 112 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 113 through 115 or (resid 116 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 117 through 120 or (resid 121 through 123 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 124 through 127  \ 
or (resid 128 and (name N or name CA or name C or name O or name CB )) or resid  \ 
129 through 151 or (resid 152 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 153 through 160 or (resid 161 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 162 through 167 or (resid 168 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 169 through 180 or (resid 181 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 182 through 228  \ 
or (resid 229 and (name N or name CA or name C or name O or name CB )) or resid  \ 
230 through 235 or (resid 236 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 237 or (resid 238 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 239 or (resid 240 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 241 through 255))
}

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 group one per residue
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:             1.180
  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:          2.630
  Check model and map are aligned:         0.110
  Set scattering table:                    0.070
  Process input model:                     23.290
  Find NCS groups from input model:        0.530
  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:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
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      :  0.011   0.046   7276  Z= 0.726
  Angle     :  1.782   8.724   9879  Z= 1.173
  Chirality :  0.088   0.494   1199
  Planarity :  0.013   0.112   1278
  Dihedral  : 14.331  89.392   2570
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 0.50
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  3.94 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  7.10 %
    Favored  : 91.12 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -1.08 (0.25), residues: 965
  helix: -0.89 (0.27), residues: 283
  sheet:  0.47 (0.29), residues: 294
  loop : -1.42 (0.28), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.092   0.020   TRP F  28 
 HIS   0.017   0.004   HIS G 153 
 PHE   0.056   0.009   PHE A 441 
 TYR   0.114   0.024   TYR F 211 
 ARG   0.012   0.001   ARG E 146 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: A  408 PHE cc_start: 0.7673 (m-80) cc_final: 0.7179 (m-80)
REVERT: A  441 PHE cc_start: 0.8098 (m-80) cc_final: 0.7817 (m-10)
REVERT: A  465 GLN cc_start: 0.8503 (pm20) cc_final: 0.8233 (pm20)
REVERT: E    1 MET cc_start: 0.5972 (tmm) cc_final: 0.4795 (tmm)
REVERT: E   24 ASN cc_start: 0.8208 (m-40) cc_final: 0.7996 (m-40)
REVERT: G   40 MET cc_start: 0.8316 (tpp) cc_final: 0.7809 (tpp)
REVERT: G   49 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8366 (tt0)
  outliers start: 13
  outliers final: 3
  residues processed: 137
  average time/residue: 0.2066
  time to fit residues: 37.0254
Evaluate side-chains
  95 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** F  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 184 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7276  Z= 0.197
  Angle     :  0.651   7.042   9879  Z= 0.350
  Chirality :  0.044   0.185   1199
  Planarity :  0.004   0.036   1278
  Dihedral  :  4.797  20.838   1025
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  4.10 %
    Favored  : 95.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.61 (0.27), residues: 965
  helix:  1.08 (0.31), residues: 281
  sheet:  0.88 (0.27), residues: 356
  loop : -0.66 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G  28 
 HIS   0.003   0.001   HIS E 246 
 PHE   0.016   0.001   PHE F 169 
 TYR   0.016   0.002   TYR G 239 
 ARG   0.003   0.001   ARG F 146 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A  408 PHE cc_start: 0.7623 (m-80) cc_final: 0.7204 (m-80)
REVERT: A  465 GLN cc_start: 0.8479 (pm20) cc_final: 0.8136 (pm20)
REVERT: F   68 MET cc_start: 0.6616 (ppp) cc_final: 0.6327 (ppp)
REVERT: G   25 GLU cc_start: 0.7895 (tp30) cc_final: 0.7623 (tt0)
REVERT: G  119 MET cc_start: 0.6662 (pmm) cc_final: 0.6049 (pmm)
  outliers start: 2
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1857
  time to fit residues: 31.5688
Evaluate side-chains
  89 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 95 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
E 179 ASN
G 184 GLN
G 204 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7276  Z= 0.196
  Angle     :  0.602   7.331   9879  Z= 0.315
  Chirality :  0.043   0.191   1199
  Planarity :  0.004   0.034   1278
  Dihedral  :  4.348  19.421   1025
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.91 (0.28), residues: 965
  helix:  1.54 (0.32), residues: 280
  sheet:  0.94 (0.27), residues: 357
  loop : -0.54 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G  28 
 HIS   0.004   0.001   HIS E 246 
 PHE   0.012   0.001   PHE G 207 
 TYR   0.016   0.002   TYR G 239 
 ARG   0.003   0.000   ARG F 146 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
REVERT: A  408 PHE cc_start: 0.7574 (m-80) cc_final: 0.7204 (m-80)
REVERT: E  177 ASN cc_start: 0.7767 (t0) cc_final: 0.7494 (t0)
REVERT: F   25 GLU cc_start: 0.7944 (mm-30) cc_final: 0.6769 (mm-30)
REVERT: G  119 MET cc_start: 0.6234 (pmm) cc_final: 0.5944 (pmm)
REVERT: G  184 GLN cc_start: 0.7464 (tp-100) cc_final: 0.7160 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1982
  time to fit residues: 30.7018
Evaluate side-chains
  87 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 66 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0370
   chunk 59 optimal weight:    4.9990
   chunk 88 optimal weight:    0.8980
   chunk 93 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
G 131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7276  Z= 0.166
  Angle     :  0.579   7.826   9879  Z= 0.301
  Chirality :  0.043   0.186   1199
  Planarity :  0.004   0.041   1278
  Dihedral  :  4.154  22.181   1025
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.01 (0.28), residues: 965
  helix:  1.65 (0.32), residues: 281
  sheet:  0.94 (0.27), residues: 359
  loop : -0.45 (0.36), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP G  28 
 HIS   0.003   0.001   HIS E 246 
 PHE   0.010   0.001   PHE G 207 
 TYR   0.013   0.001   TYR F 239 
 ARG   0.003   0.000   ARG E 146 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A  408 PHE cc_start: 0.7555 (m-80) cc_final: 0.7249 (m-80)
REVERT: E  175 LEU cc_start: 0.8373 (mp) cc_final: 0.8148 (mp)
REVERT: E  177 ASN cc_start: 0.7741 (t0) cc_final: 0.7497 (t0)
REVERT: F   25 GLU cc_start: 0.7873 (mm-30) cc_final: 0.6668 (mm-30)
REVERT: F  133 TYR cc_start: 0.6937 (m-80) cc_final: 0.6729 (m-80)
REVERT: F  150 ASP cc_start: 0.8176 (m-30) cc_final: 0.7913 (m-30)
REVERT: G  184 GLN cc_start: 0.7587 (tp-100) cc_final: 0.7095 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1708
  time to fit residues: 27.3197
Evaluate side-chains
  89 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 1 optimal weight:    7.9990
   chunk 69 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 80 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
G 131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7276  Z= 0.343
  Angle     :  0.703   9.819   9879  Z= 0.360
  Chirality :  0.046   0.194   1199
  Planarity :  0.004   0.042   1278
  Dihedral  :  4.667  19.931   1025
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.59 (0.28), residues: 965
  helix:  1.41 (0.32), residues: 281
  sheet:  0.55 (0.26), residues: 365
  loop : -0.61 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G  28 
 HIS   0.007   0.001   HIS G 246 
 PHE   0.017   0.002   PHE E 207 
 TYR   0.027   0.003   TYR G 239 
 ARG   0.002   0.000   ARG F 210 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.878 
Fit side-chains
REVERT: E  177 ASN cc_start: 0.8038 (t0) cc_final: 0.7784 (t0)
REVERT: F   25 GLU cc_start: 0.8068 (mm-30) cc_final: 0.6855 (tt0)
REVERT: F  150 ASP cc_start: 0.8254 (m-30) cc_final: 0.7984 (m-30)
REVERT: G  184 GLN cc_start: 0.7811 (tp-100) cc_final: 0.7344 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1927
  time to fit residues: 26.7872
Evaluate side-chains
  77 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 84 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 93 optimal weight:    0.8980
   chunk 77 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 90 optimal weight:    8.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
G 131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7276  Z= 0.188
  Angle     :  0.606   6.137   9879  Z= 0.310
  Chirality :  0.043   0.185   1199
  Planarity :  0.004   0.044   1278
  Dihedral  :  4.330  20.051   1025
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.75 (0.28), residues: 965
  helix:  1.63 (0.33), residues: 279
  sheet:  0.68 (0.27), residues: 356
  loop : -0.62 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G  28 
 HIS   0.003   0.001   HIS G 246 
 PHE   0.011   0.001   PHE F 214 
 TYR   0.013   0.002   TYR G 239 
 ARG   0.002   0.000   ARG E  61 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.827 
Fit side-chains
REVERT: E   65 ASN cc_start: 0.7201 (p0) cc_final: 0.6567 (p0)
REVERT: E  177 ASN cc_start: 0.7903 (t0) cc_final: 0.7629 (t0)
REVERT: E  199 MET cc_start: 0.6743 (tmm) cc_final: 0.6468 (tmm)
REVERT: F   25 GLU cc_start: 0.7881 (mm-30) cc_final: 0.6868 (mm-30)
REVERT: F  150 ASP cc_start: 0.8235 (m-30) cc_final: 0.7920 (m-30)
REVERT: G   21 ASP cc_start: 0.7290 (p0) cc_final: 0.7036 (p0)
REVERT: G  184 GLN cc_start: 0.7736 (tp-100) cc_final: 0.7207 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.2029
  time to fit residues: 29.7950
Evaluate side-chains
  84 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0980
   chunk 79 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
G 131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7276  Z= 0.173
  Angle     :  0.595   6.115   9879  Z= 0.303
  Chirality :  0.043   0.189   1199
  Planarity :  0.003   0.046   1278
  Dihedral  :  4.146  18.119   1025
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.85 (0.28), residues: 965
  helix:  1.75 (0.33), residues: 279
  sheet:  0.80 (0.27), residues: 353
  loop : -0.68 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP F  28 
 HIS   0.003   0.001   HIS E 246 
 PHE   0.016   0.001   PHE A 441 
 TYR   0.011   0.001   TYR F  60 
 ARG   0.002   0.000   ARG G   5 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A  465 GLN cc_start: 0.8101 (pm20) cc_final: 0.7681 (pm20)
REVERT: E  146 ARG cc_start: 0.7824 (tpt170) cc_final: 0.7329 (tpt170)
REVERT: E  177 ASN cc_start: 0.7892 (t0) cc_final: 0.7687 (t0)
REVERT: E  199 MET cc_start: 0.6623 (tmm) cc_final: 0.6290 (tmm)
REVERT: F   25 GLU cc_start: 0.7712 (mm-30) cc_final: 0.6912 (tp30)
REVERT: F   70 VAL cc_start: 0.8892 (m) cc_final: 0.8544 (p)
REVERT: F  150 ASP cc_start: 0.8234 (m-30) cc_final: 0.7922 (m-30)
REVERT: G   21 ASP cc_start: 0.7182 (p0) cc_final: 0.6915 (p0)
REVERT: G  184 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7224 (tp40)
REVERT: G  250 TYR cc_start: 0.7806 (m-80) cc_final: 0.7551 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1814
  time to fit residues: 27.9576
Evaluate side-chains
  89 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   chunk 85 optimal weight:    0.0670
   chunk 89 optimal weight:    0.6980
   chunk 81 optimal weight:    6.9990
   overall best weight:    1.7524

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

Flipped N/Q/H residues before XYZ refinement:
G 131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7276  Z= 0.255
  Angle     :  0.632   6.888   9879  Z= 0.324
  Chirality :  0.044   0.188   1199
  Planarity :  0.004   0.041   1278
  Dihedral  :  4.368  18.968   1025
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.68 (0.28), residues: 965
  helix:  1.63 (0.33), residues: 279
  sheet:  0.63 (0.27), residues: 357
  loop : -0.72 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G  28 
 HIS   0.004   0.001   HIS G 246 
 PHE   0.022   0.002   PHE F 214 
 TYR   0.017   0.002   TYR G 239 
 ARG   0.006   0.001   ARG F 210 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
REVERT: E   65 ASN cc_start: 0.7240 (p0) cc_final: 0.6536 (p0)
REVERT: E  146 ARG cc_start: 0.7888 (tpt170) cc_final: 0.7285 (tpt170)
REVERT: E  177 ASN cc_start: 0.7983 (t0) cc_final: 0.7772 (t0)
REVERT: E  199 MET cc_start: 0.6627 (tmm) cc_final: 0.6257 (tmm)
REVERT: F  150 ASP cc_start: 0.8275 (m-30) cc_final: 0.7995 (m-30)
REVERT: G   21 ASP cc_start: 0.7246 (p0) cc_final: 0.6981 (p0)
REVERT: G  184 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7408 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1797
  time to fit residues: 26.6249
Evaluate side-chains
  87 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0030
   chunk 92 optimal weight:    4.9990
   overall best weight:    1.5996

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

Flipped N/Q/H residues before XYZ refinement:
G 131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7276  Z= 0.241
  Angle     :  0.638   6.128   9879  Z= 0.327
  Chirality :  0.044   0.188   1199
  Planarity :  0.004   0.042   1278
  Dihedral  :  4.395  21.796   1025
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.61 (0.28), residues: 965
  helix:  1.59 (0.33), residues: 279
  sheet:  0.58 (0.26), residues: 357
  loop : -0.76 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G  28 
 HIS   0.004   0.001   HIS G 246 
 PHE   0.020   0.002   PHE A 441 
 TYR   0.017   0.002   TYR E 249 
 ARG   0.004   0.000   ARG E 149 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.814 
Fit side-chains
REVERT: E  146 ARG cc_start: 0.7890 (tpt170) cc_final: 0.7248 (tpt170)
REVERT: E  177 ASN cc_start: 0.7976 (t0) cc_final: 0.7756 (t0)
REVERT: E  199 MET cc_start: 0.6753 (tmm) cc_final: 0.6372 (tmm)
REVERT: F   25 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7071 (mm-30)
REVERT: F  150 ASP cc_start: 0.8274 (m-30) cc_final: 0.7983 (m-30)
REVERT: G   21 ASP cc_start: 0.7276 (p0) cc_final: 0.6966 (p0)
REVERT: G  184 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7478 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1697
  time to fit residues: 25.0436
Evaluate side-chains
  85 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 96 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 76 optimal weight:    0.5980
   chunk 7 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 81 optimal weight:   10.0000
   overall best weight:    1.4182

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

Flipped N/Q/H residues before XYZ refinement:
G 131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7276  Z= 0.226
  Angle     :  0.630   6.436   9879  Z= 0.323
  Chirality :  0.044   0.186   1199
  Planarity :  0.004   0.041   1278
  Dihedral  :  4.326  19.704   1025
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.62 (0.28), residues: 965
  helix:  1.62 (0.33), residues: 279
  sheet:  0.54 (0.27), residues: 358
  loop : -0.73 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G  28 
 HIS   0.004   0.001   HIS G 246 
 PHE   0.018   0.002   PHE A 441 
 TYR   0.017   0.002   TYR E 249 
 ARG   0.004   0.000   ARG E 149 

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

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

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1930 Ramachandran restraints generated.
    965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.924 
Fit side-chains
REVERT: E  146 ARG cc_start: 0.7874 (tpt170) cc_final: 0.7216 (tpt170)
REVERT: E  177 ASN cc_start: 0.7970 (t0) cc_final: 0.7757 (t0)
REVERT: E  199 MET cc_start: 0.6605 (tmm) cc_final: 0.6111 (tmm)
REVERT: F   25 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7080 (mm-30)
REVERT: F  150 ASP cc_start: 0.8259 (m-30) cc_final: 0.7960 (m-30)
REVERT: G   21 ASP cc_start: 0.7271 (p0) cc_final: 0.6967 (p0)
REVERT: G  184 GLN cc_start: 0.7904 (tp-100) cc_final: 0.7456 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1753
  time to fit residues: 25.5148
Evaluate side-chains
  83 residues out of total 852 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 21 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9980
   chunk 67 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 274 HIS
G 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.124419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.102795 restraints weight = 15764.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.103678 restraints weight = 12377.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.104100 restraints weight = 11178.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7276  Z= 0.253
  Angle     :  0.649   6.510   9879  Z= 0.333
  Chirality :  0.044   0.188   1199
  Planarity :  0.004   0.040   1278
  Dihedral  :  4.412  20.841   1025
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.54 (0.28), residues: 965
  helix:  1.59 (0.33), residues: 279
  sheet:  0.46 (0.27), residues: 358
  loop : -0.76 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G  28 
 HIS   0.005   0.001   HIS G 246 
 PHE   0.033   0.002   PHE F 214 
 TYR   0.018   0.002   TYR E 249 
 ARG   0.002   0.000   ARG F 210 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1592.66 seconds
wall clock time: 30 minutes 0.03 seconds (1800.03 seconds total)