Starting phenix.real_space_refine
on Fri Oct 10 13:18:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tgm_41241/10_2025/8tgm_41241_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tgm_41241/10_2025/8tgm_41241.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tgm_41241/10_2025/8tgm_41241.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tgm_41241/10_2025/8tgm_41241.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tgm_41241/10_2025/8tgm_41241_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tgm_41241/10_2025/8tgm_41241_trim.cif"
  }
  resolution = 3.5
  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=   0.001 sd=   0.023
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      58      5.16       5
     C    3878      2.51       5
     N     900      2.21       5
     O     990      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5826
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2869
          Classifications: {'peptide': 384}
          Link IDs: {'PTRANS': 21, 'TRANS': 362}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2869
          Classifications: {'peptide': 384}
          Link IDs: {'PTRANS': 21, 'TRANS': 362}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'YHR': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'YHR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.59, per 1000 atoms: 0.27
  Number of scatterers: 5826
  At special positions: 0
  Unit cell: (73.04, 65.736, 114.872, 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      58     16.00
     O     990      8.00
     N     900      7.00
     C    3878      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: 0.56
  Conformation dependent library (CDL) restraints added in 351.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1368

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 0 sheets defined
      90.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 40
      removed outlier: 3.738A  pdb=" N   VAL A  25 " --> pdb=" O   GLN A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 54
    Processing helix  chain 'A' and resid 131 through 144
      removed outlier: 4.004A  pdb=" N   GLU A 135 " --> pdb=" O   PHE A 131 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   THR A 137 " --> pdb=" O   GLU A 133 " (cutoff:3.500A)
      removed outlier: 5.252A  pdb=" N   ARG A 138 " --> pdb=" O   GLU A 134 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE A 143 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ALA A 144 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 165
      Proline residue:  A 155  - end of helix
      removed outlier: 4.369A  pdb=" N   GLY A 158 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 166 through 187
    Processing helix  chain 'A' and resid 189 through 219
      removed outlier: 3.683A  pdb=" N   LEU A 193 " --> pdb=" O   THR A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 254
      removed outlier: 4.082A  pdb=" N   ARG A 227 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA A 232 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   LEU A 240 " --> pdb=" O   LEU A 236 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU A 241 " --> pdb=" O   ALA A 237 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   VAL A 242 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ALA A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      Proline residue:  A 245  - end of helix
      removed outlier: 4.051A  pdb=" N   SER A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   VAL A 249 " --> pdb=" O   PRO A 245 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLU A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE A 253 " --> pdb=" O   VAL A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 276
      removed outlier: 3.533A  pdb=" N   LEU A 261 " --> pdb=" O   SER A 257 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   CYS A 276 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 297
    Processing helix  chain 'A' and resid 299 through 318
      removed outlier: 3.895A  pdb=" N   ALA A 305 " --> pdb=" O   TYR A 301 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   GLY A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   VAL A 316 " --> pdb=" O   ALA A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 330
    Processing helix  chain 'A' and resid 334 through 341
      removed outlier: 3.877A  pdb=" N   LEU A 338 " --> pdb=" O   LYS A 335 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   GLY A 339 " --> pdb=" O   TRP A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 364
      removed outlier: 3.664A  pdb=" N   TYR A 349 " --> pdb=" O   ALA A 345 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   ASN A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   LYS A 362 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   MET A 363 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 383
      removed outlier: 3.542A  pdb=" N   LEU A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL A 376 " --> pdb=" O   GLY A 372 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 386
      No H-bonds generated for 'chain 'A' and resid 384 through 386'
    Processing helix  chain 'A' and resid 388 through 391
    Processing helix  chain 'A' and resid 392 through 422
      removed outlier: 4.155A  pdb=" N   MET A 411 " --> pdb=" O   ASP A 407 " (cutoff:3.500A)
      Proline residue:  A 412  - end of helix
    Processing helix  chain 'A' and resid 427 through 455
      Proline residue:  A 445  - end of helix
    Processing helix  chain 'A' and resid 456 through 472
      removed outlier: 3.692A  pdb=" N   LEU A 460 " --> pdb=" O   GLY A 456 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   MET A 461 " --> pdb=" O   PHE A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 479
      removed outlier: 3.535A  pdb=" N   ARG A 479 " --> pdb=" O   TYR A 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 54
      removed outlier: 3.971A  pdb=" N   VAL B  23 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU B  24 " --> pdb=" O   ARG B  20 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   VAL B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   VAL B  42 " --> pdb=" O   PHE B  38 " (cutoff:3.500A)
      Proline residue:  B  43  - end of helix
      Proline residue:  B  46  - end of helix
      removed outlier: 3.720A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 165
      removed outlier: 4.098A  pdb=" N   GLU B 135 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   THR B 137 " --> pdb=" O   GLU B 133 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   ARG B 138 " --> pdb=" O   GLU B 134 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE B 143 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA B 144 " --> pdb=" O   GLY B 140 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   SER B 145 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   LYS B 146 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ALA B 147 " --> pdb=" O   PHE B 143 " (cutoff:3.500A)
      Proline residue:  B 155  - end of helix
      removed outlier: 4.338A  pdb=" N   GLY B 158 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      Proline residue:  B 159  - end of helix
    Processing helix  chain 'B' and resid 166 through 187
      removed outlier: 3.523A  pdb=" N   MET B 170 " --> pdb=" O   TYR B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 219
      removed outlier: 3.861A  pdb=" N   LEU B 193 " --> pdb=" O   THR B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 244
      removed outlier: 3.765A  pdb=" N   GLY B 226 " --> pdb=" O   ASP B 222 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ARG B 227 " --> pdb=" O   HIS B 223 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU B 236 " --> pdb=" O   ALA B 232 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ALA B 237 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 254
      removed outlier: 3.782A  pdb=" N   GLU B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE B 253 " --> pdb=" O   VAL B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 276
      removed outlier: 3.593A  pdb=" N   LEU B 261 " --> pdb=" O   SER B 257 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   CYS B 276 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 297
    Processing helix  chain 'B' and resid 299 through 318
      removed outlier: 3.511A  pdb=" N   ALA B 305 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLY B 315 " --> pdb=" O   PHE B 311 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   VAL B 316 " --> pdb=" O   ALA B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 330
    Processing helix  chain 'B' and resid 338 through 341
      removed outlier: 3.505A  pdb=" N   ALA B 341 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 338 through 341'
    Processing helix  chain 'B' and resid 342 through 360
      removed outlier: 3.835A  pdb=" N   TYR B 349 " --> pdb=" O   ALA B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 383
      removed outlier: 3.522A  pdb=" N   CYS B 368 " --> pdb=" O   GLY B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 386
      No H-bonds generated for 'chain 'B' and resid 384 through 386'
    Processing helix  chain 'B' and resid 388 through 391
    Processing helix  chain 'B' and resid 392 through 422
      removed outlier: 4.115A  pdb=" N   MET B 411 " --> pdb=" O   ASP B 407 " (cutoff:3.500A)
      Proline residue:  B 412  - end of helix
    Processing helix  chain 'B' and resid 427 through 455
      removed outlier: 3.681A  pdb=" N   ILE B 432 " --> pdb=" O   SER B 428 " (cutoff:3.500A)
      Proline residue:  B 445  - end of helix
      removed outlier: 3.875A  pdb=" N   ALA B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 472
      removed outlier: 3.700A  pdb=" N   LEU B 460 " --> pdb=" O   GLY B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 479
      removed outlier: 3.634A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG B 479 " --> pdb=" O   TYR B 476 " (cutoff:3.500A)

    442 hydrogen bonds defined for protein.
    1296 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: 0.96

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 868
        1.29 -     1.42: 1554
        1.42 -     1.55: 3447
        1.55 -     1.68: 3
        1.68 -     1.81: 102
  Bond restraints: 5974
  Sorted by residual:
  bond pdb=" C   PRO A 481 "
       pdb=" O   PRO A 481 "
    ideal  model  delta    sigma   weight residual
    1.240  1.161  0.080 1.12e-02 7.97e+03 5.06e+01
  bond pdb=" C31 YHR A 601 "
       pdb=" O30 YHR A 601 "
    ideal  model  delta    sigma   weight residual
    1.326  1.406 -0.080 2.00e-02 2.50e+03 1.60e+01
  bond pdb=" C31 YHR B 601 "
       pdb=" O30 YHR B 601 "
    ideal  model  delta    sigma   weight residual
    1.326  1.403 -0.077 2.00e-02 2.50e+03 1.47e+01
  bond pdb=" C17 YHR B 601 "
       pdb=" O19 YHR B 601 "
    ideal  model  delta    sigma   weight residual
    1.325  1.399 -0.074 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" C   PRO B 481 "
       pdb=" O   PRO B 481 "
    ideal  model  delta    sigma   weight residual
    1.240  1.200  0.041 1.12e-02 7.97e+03 1.33e+01
  ... (remaining 5969 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.77: 8048
        3.77 -     7.54: 80
        7.54 -    11.31: 10
       11.31 -    15.07: 0
       15.07 -    18.84: 2
  Bond angle restraints: 8140
  Sorted by residual:
  angle pdb=" C   PRO B 482 "
        pdb=" CA  PRO B 482 "
        pdb=" CB  PRO B 482 "
      ideal   model   delta    sigma   weight residual
     111.46  102.41    9.05 1.29e+00 6.01e-01 4.92e+01
  angle pdb=" N   ARG B 225 "
        pdb=" CA  ARG B 225 "
        pdb=" C   ARG B 225 "
      ideal   model   delta    sigma   weight residual
     111.28  104.37    6.91 1.09e+00 8.42e-01 4.02e+01
  angle pdb=" C7  YHR A 601 "
        pdb=" N8  YHR A 601 "
        pdb=" C9  YHR A 601 "
      ideal   model   delta    sigma   weight residual
     111.89  130.73  -18.84 3.00e+00 1.11e-01 3.95e+01
  angle pdb=" C7  YHR B 601 "
        pdb=" N8  YHR B 601 "
        pdb=" C9  YHR B 601 "
      ideal   model   delta    sigma   weight residual
     111.89  130.67  -18.78 3.00e+00 1.11e-01 3.92e+01
  angle pdb=" C   PRO A 481 "
        pdb=" N   PRO A 482 "
        pdb=" CA  PRO A 482 "
      ideal   model   delta    sigma   weight residual
     120.98  115.56    5.42 1.07e+00 8.73e-01 2.56e+01
  ... (remaining 8135 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.89: 3150
       22.89 -    45.78: 333
       45.78 -    68.66: 35
       68.66 -    91.55: 14
       91.55 -   114.44: 2
  Dihedral angle restraints: 3534
    sinusoidal: 1380
      harmonic: 2154
  Sorted by residual:
  dihedral pdb=" C   PRO B 482 "
           pdb=" N   PRO B 482 "
           pdb=" CA  PRO B 482 "
           pdb=" CB  PRO B 482 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -110.63  -10.07     0      2.50e+00 1.60e-01 1.62e+01
  dihedral pdb=" C13 YHR A 601 "
           pdb=" C7  YHR A 601 "
           pdb=" N8  YHR A 601 "
           pdb=" C6  YHR A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.66  -56.78  114.44     1      3.00e+01 1.11e-03 1.51e+01
  dihedral pdb=" C13 YHR B 601 "
           pdb=" C7  YHR B 601 "
           pdb=" N8  YHR B 601 "
           pdb=" C6  YHR B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.66  -56.10  113.76     1      3.00e+01 1.11e-03 1.50e+01
  ... (remaining 3531 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 874
       0.082 -    0.165: 93
       0.165 -    0.247: 4
       0.247 -    0.329: 1
       0.329 -    0.411: 2
  Chirality restraints: 974
  Sorted by residual:
  chirality pdb=" C13 YHR A 601 "
            pdb=" C12 YHR A 601 "
            pdb=" C14 YHR A 601 "
            pdb=" N8  YHR A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.70    0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" C13 YHR B 601 "
            pdb=" C12 YHR B 601 "
            pdb=" C14 YHR B 601 "
            pdb=" N8  YHR B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.69    0.40 2.00e-01 2.50e+01 3.99e+00
  chirality pdb=" CA  PHE A 131 "
            pdb=" N   PHE A 131 "
            pdb=" C   PHE A 131 "
            pdb=" CB  PHE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.93e+00
  ... (remaining 971 not shown)

  Planarity restraints: 988
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 472 "    0.062 5.00e-02 4.00e+02   9.41e-02 1.42e+01
        pdb=" N   PRO B 473 "   -0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO B 473 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO B 473 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 426 "    0.015 2.00e-02 2.50e+03   2.16e-02 9.33e+00
        pdb=" CG  TYR A 426 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 426 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 426 "    0.020 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 426 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 426 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 426 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 426 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  42 "    0.049 5.00e-02 4.00e+02   7.51e-02 9.03e+00
        pdb=" N   PRO B  43 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO B  43 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B  43 "    0.041 5.00e-02 4.00e+02
  ... (remaining 985 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1653
        2.80 -     3.33: 5569
        3.33 -     3.85: 9526
        3.85 -     4.38: 10285
        4.38 -     4.90: 18577
  Nonbonded interactions: 45610
  Sorted by model distance:
  nonbonded pdb=" O   THR B 291 "
            pdb=" OG1 THR B 291 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OE1 GLU A 135 "
            pdb=" NH1 ARG A 138 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   ARG A 365 "
            pdb=" OG  SER A 409 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   GLY A 158 "
            pdb=" OG1 THR A 161 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" OG1 THR A 291 "
            pdb=" O   THR A 423 "
     model   vdw
     2.347 3.040
  ... (remaining 45605 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             4.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.600
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
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      :  0.007   0.080   5974  Z= 0.348
  Angle     :  0.973  18.843   8140  Z= 0.523
  Chirality :  0.052   0.411    974
  Planarity :  0.009   0.094    988
  Dihedral  : 17.986 114.441   2166
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.04 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 32.41 %
    Favored  : 66.94 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.63 (0.30), residues: 756
  helix:  1.09 (0.21), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.73 (0.41), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 479 
 TYR   0.052   0.002   TYR A 426 
 PHE   0.019   0.002   PHE B 265 
 TRP   0.009   0.001   TRP A 336 
 HIS   0.005   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00655 ( 5974)
  covalent geometry    : angle       0.97298 ( 8140)
  hydrogen bonds       : bond        0.14516 (  442)
  hydrogen bonds       : angle       5.39266 ( 1296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 137
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  439 MET cc_start: 0.8235 (tpp) cc_final: 0.7662 (mpp)
REVERT: B  163 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7453 (mtp180)
REVERT: B  229 MET cc_start: 0.7887 (mmm) cc_final: 0.7625 (mmm)
REVERT: B  373 MET cc_start: 0.7738 (mtp) cc_final: 0.7413 (mtp)
REVERT: B  482 PRO cc_start: 0.8860 (Cg_exo) cc_final: 0.8607 (Cg_endo)
  outliers start: 4
  outliers final: 3
  residues processed: 138
  average time/residue: 0.0487
  time to fit residues: 10.0321
Evaluate side-chains
  130 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  163 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.4980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
A 329 GLN
B  35 ASN
B 313 ASN
B 329 GLN
B 468 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.113649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.101678 restraints weight = 8327.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.104986 restraints weight = 3884.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.107118 restraints weight = 2203.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.108558 restraints weight = 1424.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.109492 restraints weight = 1009.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.0915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5974  Z= 0.166
  Angle     :  0.686   7.540   8140  Z= 0.330
  Chirality :  0.044   0.153    974
  Planarity :  0.006   0.060    988
  Dihedral  :  7.134  56.903    944
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 28.66 %
    Favored  : 67.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.62 (0.31), residues: 756
  helix:  1.77 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop : -1.50 (0.45), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 479 
 TYR   0.011   0.001   TYR B 476 
 PHE   0.015   0.001   PHE A 356 
 TRP   0.008   0.001   TRP B 459 
 HIS   0.001   0.000   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 5974)
  covalent geometry    : angle       0.68603 ( 8140)
  hydrogen bonds       : bond        0.05573 (  442)
  hydrogen bonds       : angle       4.24163 ( 1296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  168 ILE cc_start: 0.8188 (mp) cc_final: 0.7950 (mm)
REVERT: A  174 PHE cc_start: 0.7953 (t80) cc_final: 0.7700 (t80)
REVERT: A  381 LEU cc_start: 0.8128 (mp) cc_final: 0.7721 (mp)
REVERT: B  229 MET cc_start: 0.7605 (mmm) cc_final: 0.7198 (mmm)
REVERT: B  261 LEU cc_start: 0.7812 (mm) cc_final: 0.7577 (mm)
REVERT: B  373 MET cc_start: 0.7282 (mtp) cc_final: 0.6896 (mtp)
  outliers start: 22
  outliers final: 4
  residues processed: 147
  average time/residue: 0.0569
  time to fit residues: 12.1371
Evaluate side-chains
  134 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 130
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  240 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   chunk 72 optimal weight:    0.4980
   chunk 21 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN
B 361 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.111622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.099307 restraints weight = 8309.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.102630 restraints weight = 3821.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.104736 restraints weight = 2167.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.106233 restraints weight = 1415.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.107248 restraints weight = 1007.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5974  Z= 0.172
  Angle     :  0.666   7.368   8140  Z= 0.321
  Chirality :  0.045   0.210    974
  Planarity :  0.006   0.048    988
  Dihedral  :  6.162  51.847    938
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 26.71 %
    Favored  : 68.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.51 (0.31), residues: 756
  helix:  1.76 (0.22), residues: 608
  sheet:  None (None), residues: 0
  loop : -2.26 (0.42), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 479 
 TYR   0.012   0.001   TYR B 476 
 PHE   0.018   0.001   PHE A 356 
 TRP   0.008   0.001   TRP B 366 
 HIS   0.001   0.000   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 5974)
  covalent geometry    : angle       0.66642 ( 8140)
  hydrogen bonds       : bond        0.05416 (  442)
  hydrogen bonds       : angle       4.15714 ( 1296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  174 PHE cc_start: 0.8011 (t80) cc_final: 0.7775 (t80)
REVERT: A  340 LEU cc_start: 0.7711 (mt) cc_final: 0.7341 (mp)
REVERT: A  381 LEU cc_start: 0.8218 (mp) cc_final: 0.7923 (mp)
REVERT: B  261 LEU cc_start: 0.7811 (mm) cc_final: 0.7573 (mm)
REVERT: B  274 GLN cc_start: 0.7550 (pt0) cc_final: 0.7101 (pt0)
REVERT: B  295 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.6414 (mpp)
REVERT: B  373 MET cc_start: 0.7295 (mtp) cc_final: 0.6966 (mtp)
  outliers start: 28
  outliers final: 10
  residues processed: 151
  average time/residue: 0.0508
  time to fit residues: 11.4015
Evaluate side-chains
  140 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  447 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 4 optimal weight:    0.1980
   chunk 17 optimal weight:    0.2980
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3436 r_free = 0.3436 target = 0.114943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.104859 restraints weight = 8057.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.107612 restraints weight = 3948.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.109400 restraints weight = 2321.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.110560 restraints weight = 1546.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.111371 restraints weight = 1122.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5974  Z= 0.154
  Angle     :  0.650   8.033   8140  Z= 0.311
  Chirality :  0.044   0.154    974
  Planarity :  0.005   0.042    988
  Dihedral  :  5.880  54.216    938
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 27.69 %
    Favored  : 67.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.67 (0.31), residues: 756
  helix:  1.88 (0.22), residues: 604
  sheet:  None (None), residues: 0
  loop : -2.15 (0.42), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 479 
 TYR   0.011   0.001   TYR B 476 
 PHE   0.018   0.001   PHE B 356 
 TRP   0.007   0.001   TRP B 366 
 HIS   0.001   0.000   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5974)
  covalent geometry    : angle       0.64953 ( 8140)
  hydrogen bonds       : bond        0.05120 (  442)
  hydrogen bonds       : angle       4.08250 ( 1296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   43 PRO cc_start: 0.8470 (Cg_endo) cc_final: 0.8261 (Cg_exo)
REVERT: A  174 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7624 (t80)
REVERT: A  245 PRO cc_start: 0.8434 (Cg_endo) cc_final: 0.8200 (Cg_exo)
REVERT: A  340 LEU cc_start: 0.7753 (mt) cc_final: 0.7426 (mp)
REVERT: A  381 LEU cc_start: 0.8346 (mp) cc_final: 0.8021 (mp)
REVERT: B  254 VAL cc_start: 0.8760 (p) cc_final: 0.8545 (p)
REVERT: B  261 LEU cc_start: 0.7755 (mm) cc_final: 0.7532 (mm)
REVERT: B  295 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6446 (mpp)
REVERT: B  373 MET cc_start: 0.7202 (mtp) cc_final: 0.6853 (mtp)
  outliers start: 30
  outliers final: 15
  residues processed: 152
  average time/residue: 0.0539
  time to fit residues: 11.9231
Evaluate side-chains
  148 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 73 optimal weight:    0.4980
   chunk 47 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 200 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.111769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.101537 restraints weight = 8235.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.104238 restraints weight = 4042.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.106041 restraints weight = 2386.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.107212 restraints weight = 1604.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.107999 restraints weight = 1173.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5974  Z= 0.184
  Angle     :  0.661   6.644   8140  Z= 0.318
  Chirality :  0.045   0.157    974
  Planarity :  0.006   0.043    988
  Dihedral  :  5.726  55.594    938
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 28.66 %
    Favored  : 65.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.61 (0.31), residues: 756
  helix:  1.84 (0.22), residues: 604
  sheet:  None (None), residues: 0
  loop : -2.19 (0.42), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 479 
 TYR   0.014   0.001   TYR B 476 
 PHE   0.021   0.001   PHE B 356 
 TRP   0.008   0.001   TRP B 366 
 HIS   0.001   0.000   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 5974)
  covalent geometry    : angle       0.66133 ( 8140)
  hydrogen bonds       : bond        0.05419 (  442)
  hydrogen bonds       : angle       4.10927 ( 1296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A   43 PRO cc_start: 0.8503 (Cg_endo) cc_final: 0.8260 (Cg_exo)
REVERT: A  174 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7662 (t80)
REVERT: A  245 PRO cc_start: 0.8447 (Cg_endo) cc_final: 0.8204 (Cg_exo)
REVERT: A  340 LEU cc_start: 0.7794 (mt) cc_final: 0.7483 (mp)
REVERT: A  381 LEU cc_start: 0.8379 (mp) cc_final: 0.8101 (mp)
REVERT: A  479 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6872 (ptt-90)
REVERT: B  141 VAL cc_start: 0.7790 (p) cc_final: 0.7543 (t)
REVERT: B  261 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7602 (mm)
REVERT: B  295 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6436 (mpp)
REVERT: B  373 MET cc_start: 0.7211 (mtp) cc_final: 0.6877 (mtp)
  outliers start: 33
  outliers final: 16
  residues processed: 154
  average time/residue: 0.0559
  time to fit residues: 12.2716
Evaluate side-chains
  160 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  447 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 60 optimal weight:    0.3980
   chunk 73 optimal weight:    0.3980
   chunk 42 optimal weight:    0.6980
   chunk 63 optimal weight:    0.0770
   chunk 65 optimal weight:    0.8980
   chunk 44 optimal weight:    0.3980
   chunk 24 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 35 optimal weight:    0.4980
   overall best weight:    0.3538

-------------------------------------------------------------------------------
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 = 0.3377 r_free = 0.3377 target = 0.110501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.099688 restraints weight = 8291.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.102558 restraints weight = 4058.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.104388 restraints weight = 2391.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.105620 restraints weight = 1603.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.106453 restraints weight = 1175.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5974  Z= 0.137
  Angle     :  0.629   6.789   8140  Z= 0.303
  Chirality :  0.042   0.148    974
  Planarity :  0.005   0.047    988
  Dihedral  :  5.580  56.377    936
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 29.32 %
    Favored  : 66.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.79 (0.31), residues: 756
  helix:  1.95 (0.22), residues: 606
  sheet:  None (None), residues: 0
  loop : -2.10 (0.43), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 163 
 TYR   0.010   0.001   TYR B 476 
 PHE   0.018   0.001   PHE B 356 
 TRP   0.007   0.001   TRP B 366 
 HIS   0.001   0.000   HIS B 422 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 5974)
  covalent geometry    : angle       0.62934 ( 8140)
  hydrogen bonds       : bond        0.04880 (  442)
  hydrogen bonds       : angle       4.04528 ( 1296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7582 (p)
REVERT: A   43 PRO cc_start: 0.8549 (Cg_endo) cc_final: 0.8328 (Cg_exo)
REVERT: A  174 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7599 (t80)
REVERT: A  245 PRO cc_start: 0.8446 (Cg_endo) cc_final: 0.8244 (Cg_exo)
REVERT: A  340 LEU cc_start: 0.7745 (mt) cc_final: 0.7410 (mp)
REVERT: A  381 LEU cc_start: 0.8353 (mp) cc_final: 0.8020 (mp)
REVERT: B  245 PRO cc_start: 0.8189 (Cg_endo) cc_final: 0.7904 (Cg_exo)
REVERT: B  261 LEU cc_start: 0.7801 (mm) cc_final: 0.7583 (mm)
REVERT: B  295 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6445 (mpp)
REVERT: B  373 MET cc_start: 0.7265 (mtp) cc_final: 0.6864 (mtp)
REVERT: B  423 THR cc_start: 0.8303 (m) cc_final: 0.8010 (p)
  outliers start: 28
  outliers final: 17
  residues processed: 149
  average time/residue: 0.0550
  time to fit residues: 11.9604
Evaluate side-chains
  156 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  447 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 22 optimal weight:    0.3980
   chunk 62 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 67 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 54 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3353 r_free = 0.3353 target = 0.108867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.098047 restraints weight = 8298.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.100869 restraints weight = 4088.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.102663 restraints weight = 2431.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.103904 restraints weight = 1638.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.104774 restraints weight = 1205.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5974  Z= 0.157
  Angle     :  0.644   6.727   8140  Z= 0.310
  Chirality :  0.044   0.158    974
  Planarity :  0.005   0.038    988
  Dihedral  :  5.651  57.443    936
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 29.64 %
    Favored  : 65.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.83 (0.31), residues: 756
  helix:  1.97 (0.22), residues: 606
  sheet:  None (None), residues: 0
  loop : -2.08 (0.42), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 163 
 TYR   0.012   0.001   TYR B 476 
 PHE   0.015   0.001   PHE A 356 
 TRP   0.007   0.001   TRP B 366 
 HIS   0.001   0.000   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 5974)
  covalent geometry    : angle       0.64375 ( 8140)
  hydrogen bonds       : bond        0.05062 (  442)
  hydrogen bonds       : angle       4.04228 ( 1296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 139
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 PRO cc_start: 0.8556 (Cg_endo) cc_final: 0.8313 (Cg_exo)
REVERT: A  174 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7643 (t80)
REVERT: A  245 PRO cc_start: 0.8451 (Cg_endo) cc_final: 0.8238 (Cg_exo)
REVERT: A  340 LEU cc_start: 0.7763 (mt) cc_final: 0.7443 (mp)
REVERT: A  371 ILE cc_start: 0.8054 (mm) cc_final: 0.7676 (mt)
REVERT: A  381 LEU cc_start: 0.8357 (mp) cc_final: 0.8034 (mp)
REVERT: A  479 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6815 (ptt-90)
REVERT: B  141 VAL cc_start: 0.7699 (p) cc_final: 0.7487 (t)
REVERT: B  261 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7599 (mm)
REVERT: B  295 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6441 (mpp)
REVERT: B  373 MET cc_start: 0.7245 (mtp) cc_final: 0.6864 (mtp)
REVERT: B  423 THR cc_start: 0.8355 (m) cc_final: 0.8040 (p)
REVERT: B  428 SER cc_start: 0.7859 (p) cc_final: 0.7654 (m)
  outliers start: 32
  outliers final: 19
  residues processed: 152
  average time/residue: 0.0562
  time to fit residues: 12.3380
Evaluate side-chains
  162 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  447 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 72 optimal weight:    0.0020
   chunk 64 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 74 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.5588

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.110588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.099577 restraints weight = 8191.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.102568 restraints weight = 3942.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.104474 restraints weight = 2298.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.105740 restraints weight = 1526.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.106616 restraints weight = 1107.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5974  Z= 0.164
  Angle     :  0.647   7.152   8140  Z= 0.312
  Chirality :  0.044   0.166    974
  Planarity :  0.005   0.054    988
  Dihedral  :  5.695  58.059    936
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 30.62 %
    Favored  : 65.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.83 (0.31), residues: 756
  helix:  1.98 (0.22), residues: 606
  sheet:  None (None), residues: 0
  loop : -2.09 (0.43), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 163 
 TYR   0.013   0.001   TYR B 476 
 PHE   0.014   0.001   PHE A 356 
 TRP   0.007   0.001   TRP B 366 
 HIS   0.001   0.000   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 5974)
  covalent geometry    : angle       0.64686 ( 8140)
  hydrogen bonds       : bond        0.05118 (  442)
  hydrogen bonds       : angle       4.05003 ( 1296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 PRO cc_start: 0.8569 (Cg_endo) cc_final: 0.8332 (Cg_exo)
REVERT: A  174 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7705 (t80)
REVERT: A  340 LEU cc_start: 0.7721 (mt) cc_final: 0.7391 (mp)
REVERT: A  371 ILE cc_start: 0.8043 (mm) cc_final: 0.7655 (mt)
REVERT: A  381 LEU cc_start: 0.8364 (mp) cc_final: 0.8048 (mp)
REVERT: A  439 MET cc_start: 0.7291 (tpp) cc_final: 0.6947 (mpp)
REVERT: A  479 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6831 (ptt-90)
REVERT: B  245 PRO cc_start: 0.8182 (Cg_endo) cc_final: 0.7949 (Cg_exo)
REVERT: B  261 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7625 (mm)
REVERT: B  295 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6449 (mpp)
REVERT: B  373 MET cc_start: 0.7283 (mtp) cc_final: 0.6915 (mtp)
REVERT: B  423 THR cc_start: 0.8357 (m) cc_final: 0.8025 (p)
REVERT: B  428 SER cc_start: 0.7868 (p) cc_final: 0.7648 (m)
  outliers start: 25
  outliers final: 18
  residues processed: 150
  average time/residue: 0.0577
  time to fit residues: 12.4326
Evaluate side-chains
  157 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  447 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0970
   chunk 70 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0980
   chunk 62 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 33 optimal weight:    0.2980
   chunk 41 optimal weight:    0.4980
   overall best weight:    0.3378

-------------------------------------------------------------------------------
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 = 0.3380 r_free = 0.3380 target = 0.112188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.100832 restraints weight = 8310.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.103768 restraints weight = 4085.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.105689 restraints weight = 2426.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.106957 restraints weight = 1633.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.107874 restraints weight = 1196.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5974  Z= 0.134
  Angle     :  0.640   8.474   8140  Z= 0.307
  Chirality :  0.043   0.200    974
  Planarity :  0.006   0.075    988
  Dihedral  :  5.680  56.592    936
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 31.43 %
    Favored  : 64.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.89 (0.31), residues: 756
  helix:  2.05 (0.22), residues: 604
  sheet:  None (None), residues: 0
  loop : -2.20 (0.42), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 163 
 TYR   0.010   0.001   TYR A 190 
 PHE   0.014   0.001   PHE A 356 
 TRP   0.008   0.001   TRP B 326 
 HIS   0.001   0.000   HIS B 422 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5974)
  covalent geometry    : angle       0.64049 ( 8140)
  hydrogen bonds       : bond        0.04684 (  442)
  hydrogen bonds       : angle       4.03642 ( 1296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7633 (t80)
REVERT: A  340 LEU cc_start: 0.7727 (mt) cc_final: 0.7368 (mp)
REVERT: A  371 ILE cc_start: 0.8013 (mm) cc_final: 0.7623 (mt)
REVERT: A  381 LEU cc_start: 0.8363 (mp) cc_final: 0.8052 (mp)
REVERT: A  479 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6786 (ptt-90)
REVERT: B  245 PRO cc_start: 0.8125 (Cg_endo) cc_final: 0.7893 (Cg_exo)
REVERT: B  261 LEU cc_start: 0.7811 (mm) cc_final: 0.7581 (mm)
REVERT: B  295 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6469 (mpp)
REVERT: B  373 MET cc_start: 0.7241 (mtp) cc_final: 0.6860 (mtp)
REVERT: B  423 THR cc_start: 0.8326 (m) cc_final: 0.8020 (p)
REVERT: B  428 SER cc_start: 0.7837 (p) cc_final: 0.7621 (m)
  outliers start: 23
  outliers final: 18
  residues processed: 144
  average time/residue: 0.0562
  time to fit residues: 11.7753
Evaluate side-chains
  153 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0980
   chunk 43 optimal weight:    1.9990
   chunk 13 optimal weight:    0.4980
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0000
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.3984

-------------------------------------------------------------------------------
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 = 0.3425 r_free = 0.3425 target = 0.113903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.103026 restraints weight = 8154.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.106063 restraints weight = 3890.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.108039 restraints weight = 2247.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.109250 restraints weight = 1467.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.110144 restraints weight = 1059.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5974  Z= 0.141
  Angle     :  0.647   8.032   8140  Z= 0.310
  Chirality :  0.043   0.216    974
  Planarity :  0.006   0.072    988
  Dihedral  :  5.681  56.974    936
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 31.92 %
    Favored  : 64.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.88 (0.31), residues: 756
  helix:  2.05 (0.22), residues: 604
  sheet:  None (None), residues: 0
  loop : -2.20 (0.42), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 163 
 TYR   0.010   0.001   TYR B 476 
 PHE   0.018   0.001   PHE B 246 
 TRP   0.010   0.001   TRP B 326 
 HIS   0.001   0.000   HIS B 422 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 5974)
  covalent geometry    : angle       0.64736 ( 8140)
  hydrogen bonds       : bond        0.04730 (  442)
  hydrogen bonds       : angle       4.03050 ( 1296)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7645 (t80)
REVERT: A  340 LEU cc_start: 0.7740 (mt) cc_final: 0.7376 (mp)
REVERT: A  371 ILE cc_start: 0.8010 (mm) cc_final: 0.7617 (mt)
REVERT: A  381 LEU cc_start: 0.8372 (mp) cc_final: 0.8050 (mp)
REVERT: A  479 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6778 (ptt-90)
REVERT: B  245 PRO cc_start: 0.8107 (Cg_endo) cc_final: 0.7868 (Cg_exo)
REVERT: B  261 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7620 (mm)
REVERT: B  295 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6489 (mpp)
REVERT: B  373 MET cc_start: 0.7237 (mtp) cc_final: 0.6842 (mtp)
REVERT: B  423 THR cc_start: 0.8338 (m) cc_final: 0.8030 (p)
REVERT: B  428 SER cc_start: 0.7831 (p) cc_final: 0.7624 (m)
  outliers start: 24
  outliers final: 19
  residues processed: 140
  average time/residue: 0.0560
  time to fit residues: 11.2579
Evaluate side-chains
  153 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0030
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.4990

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.114142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.103918 restraints weight = 8003.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.106734 restraints weight = 3961.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.108528 restraints weight = 2342.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.109734 restraints weight = 1567.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.110570 restraints weight = 1133.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5974  Z= 0.154
  Angle     :  0.652   7.765   8140  Z= 0.313
  Chirality :  0.044   0.245    974
  Planarity :  0.006   0.069    988
  Dihedral  :  5.696  58.066    936
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 31.11 %
    Favored  : 64.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.85 (0.31), residues: 756
  helix:  2.02 (0.22), residues: 604
  sheet:  None (None), residues: 0
  loop : -2.20 (0.42), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 163 
 TYR   0.012   0.001   TYR B 476 
 PHE   0.019   0.001   PHE B 246 
 TRP   0.008   0.001   TRP B 326 
 HIS   0.001   0.000   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 5974)
  covalent geometry    : angle       0.65193 ( 8140)
  hydrogen bonds       : bond        0.04895 (  442)
  hydrogen bonds       : angle       4.05133 ( 1296)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1080.90 seconds
wall clock time: 19 minutes 20.05 seconds (1160.05 seconds total)