Starting phenix.real_space_refine
on Wed Mar 12 03:32:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b8t_15921/03_2025/8b8t_15921_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b8t_15921/03_2025/8b8t_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/cci-nas-00/data/ceres_data/8b8t_15921/03_2025/8b8t_15921.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b8t_15921/03_2025/8b8t_15921.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b8t_15921/03_2025/8b8t_15921_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b8t_15921/03_2025/8b8t_15921_neut.cif"
  }
  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. Time to flip 26 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.73, per 1000 atoms: 0.66
  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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.49
  Conformation dependent library (CDL) restraints added in 959.1 milliseconds
  

  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: 0.96
  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: 2.46

  Time building geometry restraints manager: 1.81 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:
        0.00 -     1.74: 6759
        1.74 -     3.49: 2609
        3.49 -     5.23: 449
        5.23 -     6.98: 53
        6.98 -     8.72: 9
  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 3.040
  nonbonded pdb=" O   ASN E  71 "
            pdb=" OG  SER E  74 "
     model   vdw
     2.566 3.040
  nonbonded pdb=" O   LEU A 331 "
            pdb=" OG  SER A 334 "
     model   vdw
     2.570 3.040
  nonbonded pdb=" O   THR G 216 "
            pdb=" OG1 THR G 219 "
     model   vdw
     2.579 3.040
  nonbonded pdb=" OG  SER F 134 "
            pdb=" OE2 GLU F 201 "
     model   vdw
     2.589 3.040
  ... (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
Time spend for trying shortcut: 0.00
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:             1.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.480
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.090
-------------------------------------------------------------------------------
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 to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.753 
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: 0.2053
  time to fit residues: 36.8995
Evaluate side-chains
  95 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 76 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 88 optimal weight:    0.8980
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.127350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.104288 restraints weight = 15455.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.105184 restraints weight = 11399.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.105916 restraints weight = 10467.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1945

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= 0.197
  Angle     :  0.655   7.253   9879  Z= 0.351
  Chirality :  0.045   0.181   1199
  Planarity :  0.004   0.036   1278
  Dihedral  :  4.754  21.281   1025
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  4.23 %
    Favored  : 95.49 %
  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:  0.65 (0.27), residues: 965
  helix:  1.10 (0.31), residues: 281
  sheet:  0.93 (0.27), residues: 356
  loop : -0.66 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G  28 
 HIS   0.002   0.001   HIS F  44 
 PHE   0.016   0.001   PHE F 169 
 TYR   0.014   0.002   TYR G 239 
 ARG   0.003   0.001   ARG F 210 

*********************** 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
  130 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 128
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A  408 PHE cc_start: 0.7464 (m-80) cc_final: 0.7085 (m-80)
REVERT: A  465 GLN cc_start: 0.8487 (pm20) cc_final: 0.8173 (pm20)
REVERT: F   24 ASN cc_start: 0.8363 (t0) cc_final: 0.8079 (t0)
REVERT: F   25 GLU cc_start: 0.7926 (mm-30) cc_final: 0.6979 (mm-30)
REVERT: F   68 MET cc_start: 0.6638 (ppp) cc_final: 0.6389 (ppp)
REVERT: G   21 ASP cc_start: 0.7271 (p0) cc_final: 0.6927 (p0)
REVERT: G   25 GLU cc_start: 0.7835 (tp30) cc_final: 0.7484 (tt0)
REVERT: G  119 MET cc_start: 0.6705 (pmm) cc_final: 0.5967 (pmm)
  outliers start: 2
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1825
  time to fit residues: 32.3269
Evaluate side-chains
  90 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 88 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 4 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 90 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 21 optimal weight:   20.0000
   chunk 1 optimal weight:    9.9990
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
G 184 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.121452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.099411 restraints weight = 16282.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.099664 restraints weight = 12769.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.100902 restraints weight = 12340.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   7276  Z= 0.389
  Angle     :  0.752  10.701   9879  Z= 0.391
  Chirality :  0.048   0.203   1199
  Planarity :  0.004   0.037   1278
  Dihedral  :  5.037  19.681   1025
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.74 %
    Favored  : 94.13 %
  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:  0.38 (0.27), residues: 965
  helix:  1.09 (0.32), residues: 281
  sheet:  0.56 (0.26), residues: 360
  loop : -0.75 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP G  28 
 HIS   0.008   0.002   HIS G 246 
 PHE   0.018   0.002   PHE G 169 
 TYR   0.030   0.003   TYR G 239 
 ARG   0.005   0.001   ARG E  61 

*********************** 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
  104 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A  465 GLN cc_start: 0.8343 (pm20) cc_final: 0.8133 (pm20)
REVERT: E  197 ILE cc_start: 0.8840 (pt) cc_final: 0.8523 (mp)
REVERT: F   24 ASN cc_start: 0.8477 (t0) cc_final: 0.8222 (t0)
REVERT: F   25 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7449 (tp30)
REVERT: G   21 ASP cc_start: 0.7309 (p0) cc_final: 0.7019 (p0)
REVERT: G  119 MET cc_start: 0.6303 (pmm) cc_final: 0.6010 (pmm)
REVERT: G  184 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7380 (tp40)
  outliers start: 1
  outliers final: 1
  residues processed: 104
  average time/residue: 0.1558
  time to fit residues: 23.2153
Evaluate side-chains
  82 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 86 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 54 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0010
   overall best weight:    0.6388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.127307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.105166 restraints weight = 15752.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.105149 restraints weight = 12452.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.105902 restraints weight = 11002.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7276  Z= 0.170
  Angle     :  0.610   8.165   9879  Z= 0.316
  Chirality :  0.043   0.187   1199
  Planarity :  0.004   0.034   1278
  Dihedral  :  4.415  20.517   1025
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.28 %
    Favored  : 96.58 %
  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:  0.72 (0.28), residues: 965
  helix:  1.47 (0.33), residues: 281
  sheet:  0.79 (0.27), residues: 348
  loop : -0.65 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP F  28 
 HIS   0.003   0.001   HIS E 246 
 PHE   0.012   0.001   PHE F 169 
 TYR   0.013   0.002   TYR F 239 
 ARG   0.003   0.000   ARG F 149 

*********************** 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
  121 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
REVERT: A  408 PHE cc_start: 0.7473 (m-80) cc_final: 0.7198 (m-80)
REVERT: E  175 LEU cc_start: 0.8421 (mp) cc_final: 0.8189 (mp)
REVERT: E  177 ASN cc_start: 0.7987 (t0) cc_final: 0.7711 (t0)
REVERT: G   21 ASP cc_start: 0.7247 (p0) cc_final: 0.6894 (p0)
REVERT: G  119 MET cc_start: 0.6226 (pmm) cc_final: 0.5843 (pmm)
REVERT: G  184 GLN cc_start: 0.7741 (tp-100) cc_final: 0.7279 (tp40)
  outliers start: 1
  outliers final: 1
  residues processed: 120
  average time/residue: 0.1723
  time to fit residues: 28.6499
Evaluate side-chains
  91 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 57 optimal weight:    7.9990
   chunk 84 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0470
   chunk 82 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.7080

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.127938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.105252 restraints weight = 15544.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.106540 restraints weight = 11826.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.107950 restraints weight = 9732.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.2816

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= 0.182
  Angle     :  0.609   6.492   9879  Z= 0.312
  Chirality :  0.043   0.183   1199
  Planarity :  0.003   0.030   1278
  Dihedral  :  4.256  20.808   1025
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  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:  0.81 (0.28), residues: 965
  helix:  1.54 (0.33), residues: 280
  sheet:  0.80 (0.27), residues: 355
  loop : -0.57 (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 E 246 
 PHE   0.013   0.001   PHE A 441 
 TYR   0.012   0.002   TYR G 239 
 ARG   0.003   0.000   ARG A 387 

*********************** 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
  111 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.838 
Fit side-chains
REVERT: E  177 ASN cc_start: 0.8008 (t0) cc_final: 0.7711 (t0)
REVERT: F   25 GLU cc_start: 0.7901 (mm-30) cc_final: 0.6952 (mm-30)
REVERT: G   21 ASP cc_start: 0.7093 (p0) cc_final: 0.6739 (p0)
REVERT: G  119 MET cc_start: 0.6318 (pmm) cc_final: 0.5947 (pmm)
REVERT: G  184 GLN cc_start: 0.7720 (tp-100) cc_final: 0.7259 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1803
  time to fit residues: 28.2674
Evaluate side-chains
  83 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 9 optimal weight:    9.9990
   chunk 70 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
E 246 HIS
F 213 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.127260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.104234 restraints weight = 15683.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.105756 restraints weight = 12774.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.107110 restraints weight = 10067.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7276  Z= 0.199
  Angle     :  0.611   6.460   9879  Z= 0.312
  Chirality :  0.044   0.181   1199
  Planarity :  0.003   0.031   1278
  Dihedral  :  4.207  19.311   1025
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  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:  0.77 (0.28), residues: 965
  helix:  1.62 (0.33), residues: 280
  sheet:  0.70 (0.27), residues: 355
  loop : -0.60 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G  28 
 HIS   0.003   0.001   HIS G 246 
 PHE   0.020   0.001   PHE E 207 
 TYR   0.014   0.002   TYR G 239 
 ARG   0.003   0.000   ARG F 146 

*********************** 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
  108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.802 
Fit side-chains
REVERT: E   61 ARG cc_start: 0.6990 (tpp80) cc_final: 0.6786 (tpp80)
REVERT: E  177 ASN cc_start: 0.8058 (t0) cc_final: 0.7759 (t0)
REVERT: F   25 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7193 (tp30)
REVERT: G   21 ASP cc_start: 0.7032 (p0) cc_final: 0.6674 (p0)
REVERT: G  119 MET cc_start: 0.6419 (pmm) cc_final: 0.6046 (pmm)
REVERT: G  184 GLN cc_start: 0.7768 (tp-100) cc_final: 0.7307 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1637
  time to fit residues: 25.0334
Evaluate side-chains
  85 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 71 optimal weight:    8.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
E 246 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 = 0.3903 r_free = 0.3903 target = 0.121551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.099567 restraints weight = 16053.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.100066 restraints weight = 12066.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.100598 restraints weight = 12377.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   7276  Z= 0.380
  Angle     :  0.725   9.503   9879  Z= 0.371
  Chirality :  0.047   0.199   1199
  Planarity :  0.004   0.030   1278
  Dihedral  :  4.769  19.791   1025
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  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:  0.38 (0.27), residues: 965
  helix:  1.27 (0.32), residues: 280
  sheet:  0.41 (0.26), residues: 360
  loop : -0.72 (0.36), residues: 325

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   0.026   0.003   PHE F 214 
 TYR   0.024   0.003   TYR G 239 
 ARG   0.003   0.001   ARG F 210 

*********************** 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
  99 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A  465 GLN cc_start: 0.8183 (pm20) cc_final: 0.7714 (pm20)
REVERT: E   61 ARG cc_start: 0.7092 (tpp80) cc_final: 0.6879 (tpp80)
REVERT: E  177 ASN cc_start: 0.8202 (t0) cc_final: 0.7916 (t0)
REVERT: F   25 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7227 (tt0)
REVERT: G    1 MET cc_start: 0.6678 (tmm) cc_final: 0.6320 (ppp)
REVERT: G   21 ASP cc_start: 0.7277 (p0) cc_final: 0.6959 (p0)
REVERT: G  184 GLN cc_start: 0.7943 (tp-100) cc_final: 0.7426 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1772
  time to fit residues: 25.0748
Evaluate side-chains
  81 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 18 optimal weight:    0.0170
   chunk 72 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 67 optimal weight:   10.0000
   chunk 95 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
E 246 HIS
** G 131 GLN ** 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 = 0.3965 r_free = 0.3965 target = 0.126028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.104376 restraints weight = 15721.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.104568 restraints weight = 11465.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.105251 restraints weight = 10735.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7276  Z= 0.185
  Angle     :  0.633   8.189   9879  Z= 0.323
  Chirality :  0.044   0.187   1199
  Planarity :  0.003   0.031   1278
  Dihedral  :  4.379  21.904   1025
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  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:  0.55 (0.28), residues: 965
  helix:  1.50 (0.33), residues: 279
  sheet:  0.48 (0.26), residues: 356
  loop : -0.66 (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   0.013   0.001   PHE A 441 
 TYR   0.013   0.002   TYR E 249 
 ARG   0.004   0.001   ARG E 146 

*********************** 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
  110 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.864 
Fit side-chains
REVERT: A  465 GLN cc_start: 0.8118 (pm20) cc_final: 0.7714 (pm20)
REVERT: E  177 ASN cc_start: 0.8095 (t0) cc_final: 0.7823 (t0)
REVERT: F   25 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7112 (mm-30)
REVERT: G   21 ASP cc_start: 0.7172 (p0) cc_final: 0.6809 (p0)
REVERT: G  184 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7385 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1542
  time to fit residues: 24.7014
Evaluate side-chains
  83 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 79 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 91 optimal weight:    0.0470
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 20 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0870
   chunk 36 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    2.2262

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

Flipped N/Q/H residues before XYZ refinement:
E 246 HIS
** G 131 GLN ** 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 = 0.3925 r_free = 0.3925 target = 0.123174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.101670 restraints weight = 15986.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.101854 restraints weight = 12219.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.102985 restraints weight = 12266.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7276  Z= 0.308
  Angle     :  0.698   7.259   9879  Z= 0.358
  Chirality :  0.046   0.191   1199
  Planarity :  0.004   0.031   1278
  Dihedral  :  4.579  19.163   1025
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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:  0.47 (0.28), residues: 965
  helix:  1.47 (0.33), residues: 280
  sheet:  0.37 (0.26), residues: 360
  loop : -0.67 (0.36), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G  28 
 HIS   0.006   0.001   HIS G 246 
 PHE   0.033   0.002   PHE F 214 
 TYR   0.019   0.002   TYR G 239 
 ARG   0.004   0.000   ARG G   5 

*********************** 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
  101 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.772 
Fit side-chains
REVERT: E  177 ASN cc_start: 0.8203 (t0) cc_final: 0.7950 (t0)
REVERT: F   25 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7072 (tt0)
REVERT: G   21 ASP cc_start: 0.7191 (p0) cc_final: 0.6879 (p0)
REVERT: G  184 GLN cc_start: 0.7944 (tp-100) cc_final: 0.7448 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1569
  time to fit residues: 22.5961
Evaluate side-chains
  86 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 19 optimal weight:    0.1980
   chunk 75 optimal weight:    2.9990
   chunk 63 optimal weight:    0.1980
   chunk 58 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 35 optimal weight:    8.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
E 246 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.126210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.104529 restraints weight = 15782.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.104843 restraints weight = 12973.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.106253 restraints weight = 10977.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.3271

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= 0.202
  Angle     :  0.650   7.687   9879  Z= 0.331
  Chirality :  0.044   0.187   1199
  Planarity :  0.003   0.033   1278
  Dihedral  :  4.372  20.836   1025
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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:  1.61 (0.33), residues: 279
  sheet:  0.49 (0.27), residues: 353
  loop : -0.69 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP F  28 
 HIS   0.003   0.001   HIS G 246 
 PHE   0.012   0.001   PHE A 441 
 TYR   0.013   0.002   TYR G 239 
 ARG   0.005   0.000   ARG G   5 

********************** 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
  111 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.823 
Fit side-chains
REVERT: E  177 ASN cc_start: 0.8111 (t0) cc_final: 0.7871 (t0)
REVERT: F   25 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7031 (tt0)
REVERT: F   70 VAL cc_start: 0.8986 (p) cc_final: 0.8528 (m)
REVERT: G   21 ASP cc_start: 0.7036 (p0) cc_final: 0.6731 (p0)
REVERT: G  184 GLN cc_start: 0.7919 (tp-100) cc_final: 0.7410 (tp40)
REVERT: G  250 TYR cc_start: 0.7979 (m-80) cc_final: 0.7740 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1669
  time to fit residues: 26.0797
Evaluate side-chains
  88 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
E 246 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 = 0.3967 r_free = 0.3967 target = 0.126117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.104185 restraints weight = 15724.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.106336 restraints weight = 12746.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.106856 restraints weight = 10509.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7276  Z= 0.205
  Angle     :  0.637   6.786   9879  Z= 0.325
  Chirality :  0.044   0.186   1199
  Planarity :  0.003   0.035   1278
  Dihedral  :  4.260  18.379   1025
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  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:  0.65 (0.28), residues: 965
  helix:  1.65 (0.33), residues: 280
  sheet:  0.51 (0.26), residues: 359
  loop : -0.65 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G  28 
 HIS   0.002   0.001   HIS G 246 
 PHE   0.017   0.002   PHE A 441 
 TYR   0.013   0.002   TYR G 239 
 ARG   0.005   0.000   ARG G   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2094.62 seconds
wall clock time: 37 minutes 15.64 seconds (2235.64 seconds total)