Starting phenix.real_space_refine
on Fri Aug 22 19:16:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b8t_15921/08_2025/8b8t_15921_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b8t_15921/08_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_15921/08_2025/8b8t_15921.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b8t_15921/08_2025/8b8t_15921.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b8t_15921/08_2025/8b8t_15921_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b8t_15921/08_2025/8b8t_15921_neut.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'TYR:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ARG:plan': 14, 'GLU:plan': 12, 'ASP:plan': 6, 'HIS:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1}
          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: {'GLU:plan': 1, 'ASN:plan1': 1, 'GLN: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: {'ASN:plan1': 1, 'GLU:plan': 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: {'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 14
  Time building chain proxies: 2.23, per 1000 atoms: 0.31
  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: 0.57
  Conformation dependent library (CDL) restraints added in 426.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.31
  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: 1.20

  Time building geometry restraints manager: 0.76 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:             0.690
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.000
  Find NCS groups from input model:        0.150
  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:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.340
-------------------------------------------------------------------------------
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= 0.671
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.012   0.001   ARG E 146 
 TYR   0.114   0.024   TYR F 211 
 PHE   0.056   0.009   PHE A 441 
 TRP   0.092   0.020   TRP F  28 
 HIS   0.017   0.004   HIS G 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.01098 ( 7276)
  covalent geometry    : angle       1.78219 ( 9879)
  hydrogen bonds       : bond        0.19574 (  418)
  hydrogen bonds       : angle       8.07910 ( 1176)

*********************** 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  : 0.286 
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: 0.7818 (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: 0.7807 (tpp)
REVERT: G   49 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8367 (tt0)
  outliers start: 13
  outliers final: 3
  residues processed: 137
  average time/residue: 0.0971
  time to fit residues: 17.5693
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  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3980 r_free = 0.3980 target = 0.127126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.104552 restraints weight = 15745.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.105183 restraints weight = 11721.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.105252 restraints weight = 10487.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.105786 restraints weight = 9704.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.106095 restraints weight = 8749.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1930

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= 0.144
  Angle     :  0.661   7.537   9879  Z= 0.355
  Chirality :  0.045   0.181   1199
  Planarity :  0.004   0.035   1278
  Dihedral  :  4.781  21.049   1025
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  4.10 %
    Favored  : 95.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.27), residues: 965
  helix:  1.06 (0.31), residues: 281
  sheet:  0.88 (0.27), residues: 356
  loop : -0.67 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 146 
 TYR   0.015   0.002   TYR G 239 
 PHE   0.016   0.001   PHE F 169 
 TRP   0.007   0.001   TRP G  28 
 HIS   0.003   0.001   HIS E 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7276)
  covalent geometry    : angle       0.66077 ( 9879)
  hydrogen bonds       : bond        0.04633 (  418)
  hydrogen bonds       : angle       5.67175 ( 1176)

*********************** 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
  129 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  408 PHE cc_start: 0.7477 (m-80) cc_final: 0.7103 (m-80)
REVERT: A  465 GLN cc_start: 0.8449 (pm20) cc_final: 0.8144 (pm20)
REVERT: F   68 MET cc_start: 0.6658 (ppp) cc_final: 0.6346 (ppp)
REVERT: G   21 ASP cc_start: 0.7274 (p0) cc_final: 0.6939 (p0)
REVERT: G   25 GLU cc_start: 0.7813 (tp30) cc_final: 0.7461 (tt0)
REVERT: G  119 MET cc_start: 0.6637 (pmm) cc_final: 0.5902 (pmm)
  outliers start: 2
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0846
  time to fit residues: 14.6534
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  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0980
   chunk 61 optimal weight:    7.9990
   chunk 73 optimal weight:    9.9990
   chunk 72 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 68 optimal weight:    6.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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 = 0.3952 r_free = 0.3952 target = 0.125126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.103236 restraints weight = 15727.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.103539 restraints weight = 11462.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.103688 restraints weight = 11068.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.104407 restraints weight = 9712.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.104622 restraints weight = 8463.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7276  Z= 0.162
  Angle     :  0.644   8.194   9879  Z= 0.336
  Chirality :  0.044   0.196   1199
  Planarity :  0.004   0.034   1278
  Dihedral  :  4.543  20.019   1025
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.27), residues: 965
  helix:  1.45 (0.32), residues: 280
  sheet:  0.79 (0.27), residues: 351
  loop : -0.65 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 146 
 TYR   0.022   0.002   TYR G 239 
 PHE   0.012   0.002   PHE E 207 
 TRP   0.010   0.001   TRP G  28 
 HIS   0.005   0.001   HIS G 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 7276)
  covalent geometry    : angle       0.64373 ( 9879)
  hydrogen bonds       : bond        0.04084 (  418)
  hydrogen bonds       : angle       5.14989 ( 1176)

*********************** 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
  109 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  408 PHE cc_start: 0.7422 (m-80) cc_final: 0.7069 (m-80)
REVERT: E  177 ASN cc_start: 0.7956 (t0) cc_final: 0.7703 (t0)
REVERT: F   25 GLU cc_start: 0.7936 (mm-30) cc_final: 0.6797 (mm-30)
REVERT: G   21 ASP cc_start: 0.7246 (p0) cc_final: 0.6899 (p0)
REVERT: G  119 MET cc_start: 0.6232 (pmm) cc_final: 0.5817 (pmm)
REVERT: G  184 GLN cc_start: 0.7683 (tp-100) cc_final: 0.7349 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0712
  time to fit residues: 10.8149
Evaluate side-chains
  87 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 52 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 30 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 96 optimal weight:    5.9990
   overall best weight:    2.0184

-------------------------------------------------------------------------------
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 = 0.3940 r_free = 0.3940 target = 0.124190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.102281 restraints weight = 15952.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.102740 restraints weight = 12145.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.103528 restraints weight = 12141.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.104239 restraints weight = 9508.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.104253 restraints weight = 8923.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7276  Z= 0.182
  Angle     :  0.658   8.699   9879  Z= 0.342
  Chirality :  0.045   0.195   1199
  Planarity :  0.004   0.034   1278
  Dihedral  :  4.616  20.096   1025
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.28), residues: 965
  helix:  1.38 (0.32), residues: 280
  sheet:  0.66 (0.26), residues: 363
  loop : -0.66 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 146 
 TYR   0.021   0.002   TYR G 239 
 PHE   0.015   0.002   PHE E 207 
 TRP   0.009   0.001   TRP G  28 
 HIS   0.005   0.001   HIS G 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 7276)
  covalent geometry    : angle       0.65811 ( 9879)
  hydrogen bonds       : bond        0.03997 (  418)
  hydrogen bonds       : angle       5.02927 ( 1176)

*********************** 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
  108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
REVERT: E  177 ASN cc_start: 0.8080 (t0) cc_final: 0.7791 (t0)
REVERT: E  244 MET cc_start: 0.8434 (tpp) cc_final: 0.8129 (tpp)
REVERT: F   25 GLU cc_start: 0.8080 (mm-30) cc_final: 0.6866 (tt0)
REVERT: F  150 ASP cc_start: 0.8164 (m-30) cc_final: 0.7892 (m-30)
REVERT: G   21 ASP cc_start: 0.7204 (p0) cc_final: 0.6912 (p0)
REVERT: G  119 MET cc_start: 0.6283 (pmm) cc_final: 0.5922 (pmm)
REVERT: G  184 GLN cc_start: 0.7720 (tp-100) cc_final: 0.7272 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0768
  time to fit residues: 11.7539
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  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 20 optimal weight:   30.0000
   chunk 86 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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 = 0.3931 r_free = 0.3931 target = 0.123504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.101719 restraints weight = 16100.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.102062 restraints weight = 12296.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.102878 restraints weight = 12472.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.103377 restraints weight = 9947.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.103661 restraints weight = 8834.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7276  Z= 0.191
  Angle     :  0.672   7.753   9879  Z= 0.346
  Chirality :  0.045   0.192   1199
  Planarity :  0.004   0.033   1278
  Dihedral  :  4.686  20.806   1025
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.27), residues: 965
  helix:  1.36 (0.32), residues: 280
  sheet:  0.58 (0.26), residues: 356
  loop : -0.79 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 387 
 TYR   0.020   0.002   TYR G 239 
 PHE   0.018   0.002   PHE E 207 
 TRP   0.009   0.001   TRP G  28 
 HIS   0.005   0.001   HIS G 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 7276)
  covalent geometry    : angle       0.67237 ( 9879)
  hydrogen bonds       : bond        0.04013 (  418)
  hydrogen bonds       : angle       5.00526 ( 1176)

*********************** 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  : 0.180 
Fit side-chains
REVERT: E  149 ARG cc_start: 0.8523 (tmm-80) cc_final: 0.8239 (ttp-110)
REVERT: E  177 ASN cc_start: 0.8111 (t0) cc_final: 0.7797 (t0)
REVERT: E  244 MET cc_start: 0.8394 (tpp) cc_final: 0.8078 (tpp)
REVERT: F   25 GLU cc_start: 0.8044 (mm-30) cc_final: 0.6881 (tt0)
REVERT: F  150 ASP cc_start: 0.8204 (m-30) cc_final: 0.7895 (m-30)
REVERT: G   21 ASP cc_start: 0.7208 (p0) cc_final: 0.6879 (p0)
REVERT: G  119 MET cc_start: 0.6557 (pmm) cc_final: 0.6148 (pmm)
REVERT: G  184 GLN cc_start: 0.7828 (tp-100) cc_final: 0.7374 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0838
  time to fit residues: 12.3275
Evaluate side-chains
  84 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0770
   chunk 43 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 85 optimal weight:   10.0000
   chunk 76 optimal weight:    0.9990
   overall best weight:    1.2146

-------------------------------------------------------------------------------
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 = 0.3961 r_free = 0.3961 target = 0.125478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.103890 restraints weight = 15799.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.104668 restraints weight = 12229.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.106909 restraints weight = 10763.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.106990 restraints weight = 8013.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.107187 restraints weight = 7378.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2846

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= 0.137
  Angle     :  0.631   5.857   9879  Z= 0.325
  Chirality :  0.044   0.184   1199
  Planarity :  0.003   0.033   1278
  Dihedral  :  4.459  19.690   1025
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.28), residues: 965
  helix:  1.52 (0.33), residues: 279
  sheet:  0.60 (0.26), residues: 353
  loop : -0.74 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 387 
 TYR   0.012   0.002   TYR F  60 
 PHE   0.019   0.002   PHE A 441 
 TRP   0.029   0.002   TRP F  28 
 HIS   0.003   0.001   HIS G 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7276)
  covalent geometry    : angle       0.63074 ( 9879)
  hydrogen bonds       : bond        0.03642 (  418)
  hydrogen bonds       : angle       4.81213 ( 1176)

*********************** 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  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: E  149 ARG cc_start: 0.8501 (tmm-80) cc_final: 0.8280 (ttp80)
REVERT: E  177 ASN cc_start: 0.8106 (t0) cc_final: 0.7818 (t0)
REVERT: F   25 GLU cc_start: 0.7918 (mm-30) cc_final: 0.6861 (tt0)
REVERT: F   70 VAL cc_start: 0.9048 (m) cc_final: 0.8614 (p)
REVERT: F  150 ASP cc_start: 0.8169 (m-30) cc_final: 0.7876 (m-30)
REVERT: G   21 ASP cc_start: 0.7169 (p0) cc_final: 0.6831 (p0)
REVERT: G  119 MET cc_start: 0.6544 (pmm) cc_final: 0.6165 (pmm)
REVERT: G  184 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7400 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0846
  time to fit residues: 12.7550
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  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 96 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:   20.0000
   chunk 79 optimal weight:    1.9990
   chunk 68 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3960 r_free = 0.3960 target = 0.125474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.103733 restraints weight = 15883.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.104320 restraints weight = 12612.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.105481 restraints weight = 11872.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.106065 restraints weight = 9435.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.107546 restraints weight = 8885.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.2945

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= 0.135
  Angle     :  0.625   5.951   9879  Z= 0.320
  Chirality :  0.044   0.191   1199
  Planarity :  0.003   0.031   1278
  Dihedral  :  4.335  21.251   1025
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.28), residues: 965
  helix:  1.55 (0.32), residues: 279
  sheet:  0.48 (0.26), residues: 357
  loop : -0.65 (0.36), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 387 
 TYR   0.011   0.002   TYR F  60 
 PHE   0.016   0.001   PHE A 441 
 TRP   0.008   0.001   TRP G  28 
 HIS   0.003   0.001   HIS G 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7276)
  covalent geometry    : angle       0.62516 ( 9879)
  hydrogen bonds       : bond        0.03513 (  418)
  hydrogen bonds       : angle       4.69404 ( 1176)

*********************** 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
  105 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  465 GLN cc_start: 0.8121 (pm20) cc_final: 0.7690 (pm20)
REVERT: E  149 ARG cc_start: 0.8515 (tmm-80) cc_final: 0.8185 (ttp80)
REVERT: E  177 ASN cc_start: 0.8116 (t0) cc_final: 0.7844 (t0)
REVERT: F   25 GLU cc_start: 0.7870 (mm-30) cc_final: 0.6875 (tt0)
REVERT: F  150 ASP cc_start: 0.8153 (m-30) cc_final: 0.7868 (m-30)
REVERT: G   21 ASP cc_start: 0.7066 (p0) cc_final: 0.6733 (p0)
REVERT: G  184 GLN cc_start: 0.7808 (tp-100) cc_final: 0.7402 (tp40)
REVERT: G  250 TYR cc_start: 0.7914 (m-80) cc_final: 0.7708 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0790
  time to fit residues: 11.8633
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  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 84 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:   20.0000
   chunk 40 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0970
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.126187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.104435 restraints weight = 15802.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.105591 restraints weight = 12990.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.106486 restraints weight = 11256.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.107122 restraints weight = 8461.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.107248 restraints weight = 7946.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.3080

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= 0.134
  Angle     :  0.632   6.050   9879  Z= 0.324
  Chirality :  0.044   0.189   1199
  Planarity :  0.003   0.031   1278
  Dihedral  :  4.284  20.385   1025
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.28), residues: 965
  helix:  1.54 (0.32), residues: 279
  sheet:  0.46 (0.26), residues: 359
  loop : -0.62 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G   5 
 TYR   0.020   0.002   TYR E 249 
 PHE   0.020   0.002   PHE A 441 
 TRP   0.007   0.001   TRP G  28 
 HIS   0.003   0.001   HIS G 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7276)
  covalent geometry    : angle       0.63245 ( 9879)
  hydrogen bonds       : bond        0.03458 (  418)
  hydrogen bonds       : angle       4.70324 ( 1176)

*********************** 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  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A  327 LEU cc_start: 0.6798 (mm) cc_final: 0.6466 (mm)
REVERT: E  177 ASN cc_start: 0.8121 (t0) cc_final: 0.7842 (t0)
REVERT: F   25 GLU cc_start: 0.7842 (mm-30) cc_final: 0.6884 (tt0)
REVERT: F  150 ASP cc_start: 0.8129 (m-30) cc_final: 0.7815 (m-30)
REVERT: G   21 ASP cc_start: 0.7116 (p0) cc_final: 0.6763 (p0)
REVERT: G  184 GLN cc_start: 0.7855 (tp-100) cc_final: 0.7381 (tp40)
REVERT: G  250 TYR cc_start: 0.7888 (m-80) cc_final: 0.7652 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0800
  time to fit residues: 11.5866
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  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 23 optimal weight:   30.0000
   chunk 61 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9980
   chunk 20 optimal weight:   30.0000
   chunk 81 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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 = 0.3956 r_free = 0.3956 target = 0.125138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.103437 restraints weight = 15748.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.104076 restraints weight = 13110.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.105294 restraints weight = 11469.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.105796 restraints weight = 8575.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.105916 restraints weight = 8279.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7276  Z= 0.164
  Angle     :  0.659   6.426   9879  Z= 0.339
  Chirality :  0.045   0.189   1199
  Planarity :  0.004   0.032   1278
  Dihedral  :  4.423  19.813   1025
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.28), residues: 965
  helix:  1.44 (0.33), residues: 279
  sheet:  0.38 (0.26), residues: 360
  loop : -0.63 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G   5 
 TYR   0.016   0.002   TYR E 249 
 PHE   0.022   0.002   PHE A 441 
 TRP   0.008   0.001   TRP G  28 
 HIS   0.005   0.001   HIS G 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 7276)
  covalent geometry    : angle       0.65906 ( 9879)
  hydrogen bonds       : bond        0.03677 (  418)
  hydrogen bonds       : angle       4.82570 ( 1176)

*********************** 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  : 0.297 
Fit side-chains
REVERT: A  327 LEU cc_start: 0.6804 (mm) cc_final: 0.6485 (mm)
REVERT: E  146 ARG cc_start: 0.8058 (tpt170) cc_final: 0.7305 (tpp-160)
REVERT: E  177 ASN cc_start: 0.8169 (t0) cc_final: 0.7895 (t0)
REVERT: F   25 GLU cc_start: 0.7879 (mm-30) cc_final: 0.6958 (tt0)
REVERT: F  150 ASP cc_start: 0.8150 (m-30) cc_final: 0.7872 (m-30)
REVERT: G   21 ASP cc_start: 0.7103 (p0) cc_final: 0.6790 (p0)
REVERT: G  184 GLN cc_start: 0.7899 (tp-100) cc_final: 0.7408 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0778
  time to fit residues: 11.0921
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  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 59 optimal weight:    0.4980
   chunk 39 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0060
   chunk 8 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.3002

-------------------------------------------------------------------------------
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 = 0.3961 r_free = 0.3961 target = 0.125773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.103818 restraints weight = 15771.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.105667 restraints weight = 13398.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.106311 restraints weight = 10891.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.106731 restraints weight = 8525.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.106928 restraints weight = 8195.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.3225

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= 0.144
  Angle     :  0.664   8.219   9879  Z= 0.341
  Chirality :  0.045   0.187   1199
  Planarity :  0.004   0.032   1278
  Dihedral  :  4.437  19.637   1025
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.27), residues: 965
  helix:  1.37 (0.32), residues: 280
  sheet:  0.38 (0.26), residues: 353
  loop : -0.66 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 149 
 TYR   0.017   0.002   TYR E 249 
 PHE   0.036   0.002   PHE F 214 
 TRP   0.008   0.001   TRP G  28 
 HIS   0.004   0.001   HIS G 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7276)
  covalent geometry    : angle       0.66369 ( 9879)
  hydrogen bonds       : bond        0.03587 (  418)
  hydrogen bonds       : angle       4.82489 ( 1176)

********************** 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
  106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  327 LEU cc_start: 0.6856 (mm) cc_final: 0.6584 (mm)
REVERT: E  146 ARG cc_start: 0.7898 (tpt170) cc_final: 0.7439 (tpt170)
REVERT: E  149 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8145 (ttp80)
REVERT: E  177 ASN cc_start: 0.8181 (t0) cc_final: 0.7902 (t0)
REVERT: F   25 GLU cc_start: 0.7871 (mm-30) cc_final: 0.6732 (tt0)
REVERT: F  150 ASP cc_start: 0.8142 (m-30) cc_final: 0.7834 (m-30)
REVERT: G   21 ASP cc_start: 0.7080 (p0) cc_final: 0.6784 (p0)
REVERT: G  184 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7468 (tp40)
REVERT: G  250 TYR cc_start: 0.7927 (m-80) cc_final: 0.7720 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0870
  time to fit residues: 12.7109
Evaluate side-chains
  87 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 9 optimal weight:    9.9990
   chunk 86 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 21 optimal weight:    9.9990
   chunk 80 optimal weight:    0.9990
   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
** 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 = 0.3970 r_free = 0.3970 target = 0.126232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.104366 restraints weight = 15738.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.105387 restraints weight = 13703.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.106674 restraints weight = 11397.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.107082 restraints weight = 8576.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.107220 restraints weight = 8404.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.3257

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= 0.137
  Angle     :  0.654   7.712   9879  Z= 0.333
  Chirality :  0.044   0.185   1199
  Planarity :  0.004   0.032   1278
  Dihedral  :  4.305  18.552   1025
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.28), residues: 965
  helix:  1.43 (0.33), residues: 280
  sheet:  0.39 (0.26), residues: 352
  loop : -0.67 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G   5 
 TYR   0.016   0.002   TYR E 249 
 PHE   0.021   0.002   PHE A 441 
 TRP   0.008   0.001   TRP G  28 
 HIS   0.003   0.001   HIS G 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 7276)
  covalent geometry    : angle       0.65353 ( 9879)
  hydrogen bonds       : bond        0.03496 (  418)
  hydrogen bonds       : angle       4.74227 ( 1176)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1161.47 seconds
wall clock time: 20 minutes 52.28 seconds (1252.28 seconds total)