Starting phenix.real_space_refine
on Wed Feb 12 03:56:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b8t_15921/02_2025/8b8t_15921_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b8t_15921/02_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_15921/02_2025/8b8t_15921.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b8t_15921/02_2025/8b8t_15921.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b8t_15921/02_2025/8b8t_15921_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b8t_15921/02_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.66, per 1000 atoms: 0.65
  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: 1.58
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.91
  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: 2.15

  Time building geometry restraints manager: 1.85 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:             2.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.000
  Set scattering table:                    0.030
  Process input model:                     19.730
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.450
-------------------------------------------------------------------------------
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  : 0.896 
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: 0.2159
  time to fit residues: 38.7489
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  : 0.810 
-------------------------------------------------------------------------------
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:    5.9990
   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 = 0.127349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.104279 restraints weight = 15455.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.105185 restraints weight = 11406.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.105916 restraints weight = 10502.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1946

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   7.254   9879  Z= 0.351
  Chirality :  0.045   0.181   1199
  Planarity :  0.004   0.036   1278
  Dihedral  :  4.754  21.283   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  : 0.805 
Fit side-chains
REVERT: A  408 PHE cc_start: 0.7463 (m-80) cc_final: 0.7085 (m-80)
REVERT: A  465 GLN cc_start: 0.8487 (pm20) cc_final: 0.8174 (pm20)
REVERT: F   24 ASN cc_start: 0.8362 (t0) cc_final: 0.8081 (t0)
REVERT: F   25 GLU cc_start: 0.7927 (mm-30) cc_final: 0.6980 (mm-30)
REVERT: F   68 MET cc_start: 0.6638 (ppp) cc_final: 0.6389 (ppp)
REVERT: G   21 ASP cc_start: 0.7269 (p0) cc_final: 0.6925 (p0)
REVERT: G   25 GLU cc_start: 0.7835 (tp30) cc_final: 0.7484 (tt0)
REVERT: G  119 MET cc_start: 0.6706 (pmm) cc_final: 0.5966 (pmm)
  outliers start: 2
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1914
  time to fit residues: 33.2104
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  : 0.812 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 4 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 21 optimal weight:   20.0000
   chunk 1 optimal weight:   10.0000
   overall best weight:    2.3388

-------------------------------------------------------------------------------
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 = 0.3929 r_free = 0.3929 target = 0.123478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.101273 restraints weight = 16150.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.101674 restraints weight = 12251.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.102735 restraints weight = 12091.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7276  Z= 0.311
  Angle     :  0.684   8.448   9879  Z= 0.357
  Chirality :  0.046   0.200   1199
  Planarity :  0.004   0.036   1278
  Dihedral  :  4.731  20.005   1025
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  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:  0.60 (0.27), residues: 965
  helix:  1.33 (0.32), residues: 280
  sheet:  0.75 (0.27), residues: 351
  loop : -0.72 (0.35), residues: 334

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   0.015   0.002   PHE G 207 
 TYR   0.026   0.003   TYR G 239 
 ARG   0.004   0.001   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
  108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
REVERT: A  408 PHE cc_start: 0.7569 (m-80) cc_final: 0.7124 (m-80)
REVERT: E   24 ASN cc_start: 0.8330 (m-40) cc_final: 0.8071 (m-40)
REVERT: E  177 ASN cc_start: 0.8029 (t0) cc_final: 0.7713 (t0)
REVERT: F   24 ASN cc_start: 0.8405 (t0) cc_final: 0.8146 (t0)
REVERT: F   25 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7352 (tp30)
REVERT: G   21 ASP cc_start: 0.7307 (p0) cc_final: 0.6938 (p0)
REVERT: G   25 GLU cc_start: 0.7895 (tp30) cc_final: 0.7668 (tt0)
REVERT: G  119 MET cc_start: 0.6283 (pmm) cc_final: 0.5927 (pmm)
REVERT: G  184 GLN cc_start: 0.7783 (tp-100) cc_final: 0.7343 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1629
  time to fit residues: 25.1897
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  : 0.846 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 86 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3989 r_free = 0.3989 target = 0.127629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.104300 restraints weight = 15731.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.105575 restraints weight = 11381.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.106918 restraints weight = 9810.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7276  Z= 0.168
  Angle     :  0.605   8.181   9879  Z= 0.313
  Chirality :  0.043   0.188   1199
  Planarity :  0.003   0.033   1278
  Dihedral  :  4.325  20.537   1025
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    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:  0.83 (0.28), residues: 965
  helix:  1.50 (0.33), residues: 281
  sheet:  0.90 (0.27), residues: 348
  loop : -0.60 (0.35), residues: 336

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   0.013   0.001   PHE E 144 
 TYR   0.013   0.002   TYR F  60 
 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
  117 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.788 
Fit side-chains
REVERT: E  175 LEU cc_start: 0.8382 (mp) cc_final: 0.8129 (mp)
REVERT: E  177 ASN cc_start: 0.7965 (t0) cc_final: 0.7672 (t0)
REVERT: F   24 ASN cc_start: 0.8383 (t0) cc_final: 0.8039 (t0)
REVERT: F   25 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7001 (tt0)
REVERT: F  150 ASP cc_start: 0.8182 (m-30) cc_final: 0.7971 (m-30)
REVERT: G   21 ASP cc_start: 0.7199 (p0) cc_final: 0.6857 (p0)
REVERT: G  184 GLN cc_start: 0.7684 (tp-100) cc_final: 0.7158 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1685
  time to fit residues: 27.6541
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  : 0.799 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 84 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 55 optimal weight:    9.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.126469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.104381 restraints weight = 15633.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.105508 restraints weight = 13559.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.107132 restraints weight = 10880.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7276  Z= 0.222
  Angle     :  0.625   6.548   9879  Z= 0.321
  Chirality :  0.044   0.186   1199
  Planarity :  0.004   0.031   1278
  Dihedral  :  4.375  20.028   1025
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  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:  0.83 (0.28), residues: 965
  helix:  1.55 (0.33), residues: 280
  sheet:  0.81 (0.27), residues: 356
  loop : -0.55 (0.36), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G  28 
 HIS   0.004   0.001   HIS G 246 
 PHE   0.020   0.002   PHE E 207 
 TYR   0.016   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
  106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.827 
Fit side-chains
REVERT: E  177 ASN cc_start: 0.8055 (t0) cc_final: 0.7745 (t0)
REVERT: E  244 MET cc_start: 0.8276 (tpp) cc_final: 0.7996 (tpp)
REVERT: F   24 ASN cc_start: 0.8298 (t0) cc_final: 0.7889 (t0)
REVERT: F   25 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7100 (tt0)
REVERT: F  150 ASP cc_start: 0.8166 (m-30) cc_final: 0.7867 (m-30)
REVERT: G   21 ASP cc_start: 0.7115 (p0) cc_final: 0.6825 (p0)
REVERT: G  184 GLN cc_start: 0.7793 (tp-100) cc_final: 0.7253 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1817
  time to fit residues: 26.8404
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  : 0.924 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 75 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 70 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.123406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.101755 restraints weight = 15940.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.102100 restraints weight = 11960.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.103530 restraints weight = 11504.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
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      :  0.005   0.048   7276  Z= 0.299
  Angle     :  0.675   8.164   9879  Z= 0.347
  Chirality :  0.046   0.189   1199
  Planarity :  0.004   0.030   1278
  Dihedral  :  4.587  19.549   1025
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  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:  0.58 (0.28), residues: 965
  helix:  1.47 (0.33), residues: 279
  sheet:  0.51 (0.26), residues: 362
  loop : -0.63 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G  28 
 HIS   0.006   0.001   HIS G 246 
 PHE   0.016   0.002   PHE E 207 
 TYR   0.021   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
  101 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.838 
Fit side-chains
REVERT: E  149 ARG cc_start: 0.8519 (tmm-80) cc_final: 0.8052 (ttp-170)
REVERT: E  177 ASN cc_start: 0.8160 (t0) cc_final: 0.7860 (t0)
REVERT: E  199 MET cc_start: 0.7003 (tmm) cc_final: 0.6462 (tmm)
REVERT: E  200 ASN cc_start: 0.7978 (m-40) cc_final: 0.7661 (m-40)
REVERT: E  244 MET cc_start: 0.8355 (tpp) cc_final: 0.8040 (tpp)
REVERT: F   24 ASN cc_start: 0.8392 (t0) cc_final: 0.7995 (t0)
REVERT: F   25 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7257 (tt0)
REVERT: G   21 ASP cc_start: 0.7192 (p0) cc_final: 0.6872 (p0)
REVERT: G  184 GLN cc_start: 0.7863 (tp-100) cc_final: 0.7414 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1784
  time to fit residues: 25.1616
Evaluate side-chains
  82 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 72 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 3 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   chunk 61 optimal weight:   20.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.120066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.098225 restraints weight = 16167.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.098464 restraints weight = 12337.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.099377 restraints weight = 12547.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   7276  Z= 0.441
  Angle     :  0.779  11.098   9879  Z= 0.402
  Chirality :  0.049   0.204   1199
  Planarity :  0.004   0.030   1278
  Dihedral  :  5.114  19.832   1025
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  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:  0.10 (0.27), residues: 965
  helix:  1.07 (0.32), residues: 280
  sheet:  0.25 (0.26), residues: 358
  loop : -0.90 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.004   TRP F  28 
 HIS   0.009   0.002   HIS G 246 
 PHE   0.030   0.003   PHE G 207 
 TYR   0.027   0.003   TYR G 239 
 ARG   0.003   0.000   ARG A 387 

*********************** 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
  102 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A  465 GLN cc_start: 0.8164 (pm20) cc_final: 0.7719 (pm20)
REVERT: E  149 ARG cc_start: 0.8530 (tmm-80) cc_final: 0.8236 (ttt-90)
REVERT: E  177 ASN cc_start: 0.8200 (t0) cc_final: 0.7802 (t0)
REVERT: E  199 MET cc_start: 0.6906 (tmm) cc_final: 0.6440 (tmm)
REVERT: E  244 MET cc_start: 0.8424 (tpp) cc_final: 0.8078 (tpp)
REVERT: F   24 ASN cc_start: 0.8503 (t0) cc_final: 0.8156 (t0)
REVERT: F   25 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7427 (tt0)
REVERT: F   70 VAL cc_start: 0.9162 (m) cc_final: 0.8772 (p)
REVERT: G    5 ARG cc_start: 0.8554 (ttt-90) cc_final: 0.8349 (ttt-90)
REVERT: G   21 ASP cc_start: 0.7381 (p0) cc_final: 0.7056 (p0)
REVERT: G  119 MET cc_start: 0.6517 (pmm) cc_final: 0.6206 (pmm)
REVERT: G  184 GLN cc_start: 0.8065 (tp-100) cc_final: 0.7545 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1791
  time to fit residues: 25.2597
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  : 0.867 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0370
   chunk 69 optimal weight:    0.8980
   chunk 61 optimal weight:    9.9990
   chunk 80 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    1.3864

-------------------------------------------------------------------------------
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 = 0.3937 r_free = 0.3937 target = 0.123955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.102500 restraints weight = 15860.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.103131 restraints weight = 12261.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.105246 restraints weight = 11216.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3109

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= 0.233
  Angle     :  0.659   8.071   9879  Z= 0.338
  Chirality :  0.045   0.193   1199
  Planarity :  0.004   0.032   1278
  Dihedral  :  4.674  22.501   1025
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  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:  0.40 (0.28), residues: 965
  helix:  1.37 (0.32), residues: 280
  sheet:  0.44 (0.27), residues: 354
  loop : -0.80 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F  28 
 HIS   0.004   0.001   HIS G 246 
 PHE   0.018   0.002   PHE G 207 
 TYR   0.013   0.002   TYR F  60 
 ARG   0.003   0.000   ARG A 387 

*********************** 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
  103 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
REVERT: E  177 ASN cc_start: 0.8163 (t0) cc_final: 0.7875 (t0)
REVERT: E  199 MET cc_start: 0.7046 (tmm) cc_final: 0.6337 (tmm)
REVERT: F   24 ASN cc_start: 0.8392 (t0) cc_final: 0.8044 (t0)
REVERT: F   25 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7330 (tt0)
REVERT: G   21 ASP cc_start: 0.7184 (p0) cc_final: 0.6864 (p0)
REVERT: G  119 MET cc_start: 0.6413 (pmm) cc_final: 0.6198 (pmm)
REVERT: G  184 GLN cc_start: 0.7983 (tp-100) cc_final: 0.7502 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1669
  time to fit residues: 24.6910
Evaluate side-chains
  82 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 37 optimal weight:    0.0070
   chunk 7 optimal weight:    9.9990
   chunk 91 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:   30.0000
   chunk 67 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0670
   chunk 36 optimal weight:    0.5980
   chunk 62 optimal weight:    4.9990
   overall best weight:    1.3340

-------------------------------------------------------------------------------
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 = 0.3947 r_free = 0.3947 target = 0.124576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.101923 restraints weight = 15855.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.103756 restraints weight = 14177.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.104951 restraints weight = 10389.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3172

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= 0.227
  Angle     :  0.651   7.845   9879  Z= 0.335
  Chirality :  0.044   0.191   1199
  Planarity :  0.004   0.031   1278
  Dihedral  :  4.532  19.670   1025
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  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:  0.50 (0.28), residues: 965
  helix:  1.48 (0.33), residues: 279
  sheet:  0.48 (0.27), residues: 359
  loop : -0.75 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G  28 
 HIS   0.004   0.001   HIS G 246 
 PHE   0.017   0.002   PHE A 441 
 TYR   0.012   0.002   TYR F  60 
 ARG   0.003   0.001   ARG A 387 

*********************** 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
  105 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.721 
Fit side-chains
REVERT: E  149 ARG cc_start: 0.8499 (tmm-80) cc_final: 0.8165 (ttp80)
REVERT: E  177 ASN cc_start: 0.8071 (t0) cc_final: 0.7823 (t0)
REVERT: E  199 MET cc_start: 0.6950 (tmm) cc_final: 0.6317 (tmm)
REVERT: F   24 ASN cc_start: 0.8389 (t0) cc_final: 0.8084 (t0)
REVERT: F   25 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7342 (tt0)
REVERT: G   21 ASP cc_start: 0.7129 (p0) cc_final: 0.6789 (p0)
REVERT: G  184 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7514 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1699
  time to fit residues: 25.2410
Evaluate side-chains
  82 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 24 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   chunk 19 optimal weight:    0.3980
   chunk 75 optimal weight:    0.0770
   chunk 63 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0040
   chunk 12 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.4750

-------------------------------------------------------------------------------
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 = 0.3984 r_free = 0.3984 target = 0.127459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.103829 restraints weight = 15928.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.106247 restraints weight = 13271.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.107454 restraints weight = 9323.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.3345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7276  Z= 0.185
  Angle     :  0.641   7.901   9879  Z= 0.326
  Chirality :  0.044   0.184   1199
  Planarity :  0.003   0.034   1278
  Dihedral  :  4.329  20.352   1025
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  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:  0.63 (0.28), residues: 965
  helix:  1.57 (0.33), residues: 279
  sheet:  0.58 (0.27), residues: 363
  loop : -0.71 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G  28 
 HIS   0.002   0.000   HIS E 246 
 PHE   0.016   0.002   PHE A 441 
 TYR   0.011   0.001   TYR F  60 
 ARG   0.003   0.000   ARG A 387 

********************** 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
  108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.919 
Fit side-chains
REVERT: A  470 THR cc_start: 0.7790 (m) cc_final: 0.7503 (p)
REVERT: E  149 ARG cc_start: 0.8469 (tmm-80) cc_final: 0.8195 (ttp80)
REVERT: E  177 ASN cc_start: 0.7985 (t0) cc_final: 0.7735 (t0)
REVERT: E  199 MET cc_start: 0.6794 (tmm) cc_final: 0.6157 (tmm)
REVERT: G   21 ASP cc_start: 0.7039 (p0) cc_final: 0.6684 (p0)
REVERT: G  184 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7441 (tp40)
REVERT: G  250 TYR cc_start: 0.7876 (m-80) cc_final: 0.7603 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1841
  time to fit residues: 27.6469
Evaluate side-chains
  89 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
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 80 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.126315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.103747 restraints weight = 15711.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.104758 restraints weight = 13900.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.106602 restraints weight = 10865.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.3383

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= 0.225
  Angle     :  0.653   7.743   9879  Z= 0.334
  Chirality :  0.044   0.185   1199
  Planarity :  0.004   0.033   1278
  Dihedral  :  4.366  18.217   1025
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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:  1.59 (0.33), residues: 279
  sheet:  0.52 (0.27), residues: 358
  loop : -0.73 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G  28 
 HIS   0.004   0.001   HIS G 246 
 PHE   0.015   0.002   PHE A 441 
 TYR   0.017   0.002   TYR E 249 
 ARG   0.003   0.000   ARG A 387 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2034.92 seconds
wall clock time: 37 minutes 37.88 seconds (2257.88 seconds total)