Starting phenix.real_space_refine
on Sat Aug 23 01:04:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fva_50794/08_2025/9fva_50794.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fva_50794/08_2025/9fva_50794.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fva_50794/08_2025/9fva_50794.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fva_50794/08_2025/9fva_50794.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fva_50794/08_2025/9fva_50794.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fva_50794/08_2025/9fva_50794.map"
  }
  resolution = 4.4
  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=   0.009
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      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 2.00, per 1000 atoms: 0.23
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (120.36, 68.68, 135.32, 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      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      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: 0.81
  Conformation dependent library (CDL) restraints added in 260.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 6 sheets defined
      62.5% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'B' and resid 15 through 20
      removed outlier: 4.502A  pdb=" N   THR B  19 " --> pdb=" O   ARG B  15 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE B  20 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 15 through 20'
    Processing helix  chain 'B' and resid 21 through 23
      No H-bonds generated for 'chain 'B' and resid 21 through 23'
    Processing helix  chain 'B' and resid 24 through 53
      removed outlier: 4.127A  pdb=" N   ILE B  28 " --> pdb=" O   LYS B  24 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   VAL B  32 " --> pdb=" O   ILE B  28 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   ALA B  33 " --> pdb=" O   VAL B  29 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ALA B  38 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ASP B  41 " --> pdb=" O   ASN B  37 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU B  48 " --> pdb=" O   MET B  44 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 62 through 65
    Processing helix  chain 'B' and resid 66 through 109
    Processing helix  chain 'B' and resid 123 through 164
      removed outlier: 3.650A  pdb=" N   SER B 132 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   GLU B 133 " --> pdb=" O   THR B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 213
      Proline residue:  B 176  - end of helix
      removed outlier: 4.016A  pdb=" N   MET B 196 " --> pdb=" O   ILE B 192 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   THR B 199 " --> pdb=" O   ASN B 195 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLN B 209 " --> pdb=" O   THR B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
      removed outlier: 3.673A  pdb=" N   VAL B 217 " --> pdb=" O   GLY B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 270
      removed outlier: 3.710A  pdb=" N   SER B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   ASP B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
      removed outlier: 3.567A  pdb=" N   LEU B 263 " --> pdb=" O   ALA B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 302
      removed outlier: 3.557A  pdb=" N   VAL B 286 " --> pdb=" O   GLY B 282 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   MET B 295 " --> pdb=" O   MET B 291 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   ARG B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
    Processing helix  chain 'B' and resid 303 through 322
    Processing helix  chain 'B' and resid 381 through 387
      removed outlier: 4.158A  pdb=" N   ALA B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 438
    Processing helix  chain 'B' and resid 446 through 458
    Processing helix  chain 'B' and resid 482 through 497
    Processing helix  chain 'B' and resid 524 through 529
    Processing helix  chain 'B' and resid 538 through 544
    Processing helix  chain 'B' and resid 561 through 568
      removed outlier: 3.989A  pdb=" N   HIS B 568 " --> pdb=" O   ASP B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 580
    Processing helix  chain 'A' and resid 15 through 21
      removed outlier: 4.509A  pdb=" N   THR A  19 " --> pdb=" O   ARG A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 47
      removed outlier: 4.182A  pdb=" N   LEU A  27 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ILE A  28 " --> pdb=" O   LYS A  24 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU A  36 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ASP A  41 " --> pdb=" O   ASN A  37 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   THR A  42 " --> pdb=" O   ALA A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 66 through 107
      removed outlier: 4.212A  pdb=" N   LEU A  77 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   THR A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   MET A  98 " --> pdb=" O   GLY A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 116
      removed outlier: 3.925A  pdb=" N   PHE A 115 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 129
    Processing helix  chain 'A' and resid 129 through 148
    Processing helix  chain 'A' and resid 151 through 158
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 168 through 195
      Proline residue:  A 176  - end of helix
    Processing helix  chain 'A' and resid 196 through 213
    Processing helix  chain 'A' and resid 213 through 221
    Processing helix  chain 'A' and resid 222 through 270
      removed outlier: 3.698A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 3.655A  pdb=" N   ILE A 258 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA A 259 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 3.620A  pdb=" N   MET A 276 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 303
      removed outlier: 4.021A  pdb=" N   THR A 285 " --> pdb=" O   ALA A 281 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   MET A 295 " --> pdb=" O   MET A 291 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 4.547A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 309
      removed outlier: 3.534A  pdb=" N   GLN A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 324
      removed outlier: 3.833A  pdb=" N   ALA A 314 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE A 321 " --> pdb=" O   THR A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 391
      removed outlier: 3.591A  pdb=" N   ILE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 419
    Processing helix  chain 'A' and resid 433 through 437
    Processing helix  chain 'A' and resid 446 through 456
      removed outlier: 3.646A  pdb=" N   ALA A 453 " --> pdb=" O   GLN A 449 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   MET A 456 " --> pdb=" O   GLU A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 486
    Processing helix  chain 'A' and resid 514 through 528
      removed outlier: 3.662A  pdb=" N   LYS A 528 " --> pdb=" O   ASP A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 545
    Processing helix  chain 'A' and resid 563 through 568
      removed outlier: 3.620A  pdb=" N   GLU A 567 " --> pdb=" O   ASN A 563 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   HIS A 568 " --> pdb=" O   ASP A 564 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 563 through 568'
    Processing helix  chain 'A' and resid 571 through 580
    Processing sheet with id=AA1, first strand: chain 'B' and resid 342 through 345
      removed outlier: 4.114A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 366 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE B 366 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 348 through 349
      removed outlier: 3.755A  pdb=" N   GLU B 397 " --> pdb=" O   THR B 348 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 502 through 504
      removed outlier: 6.423A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL B 372 " --> pdb=" O   SER B 532 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   VAL B 534 " --> pdb=" O   VAL B 372 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   VAL B 551 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   VAL B 375 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   VAL B 550 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366
    Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374
      removed outlier: 7.106A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 431 through 432
      removed outlier: 3.783A  pdb=" N   ASP A 431 " --> pdb=" O   ILE A 474 " (cutoff:3.500A)

    478 hydrogen bonds defined for protein.
    1404 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2323
        1.33 -     1.45: 1499
        1.45 -     1.58: 5024
        1.58 -     1.70: 0
        1.70 -     1.82: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" C   GLY A 110 "
       pdb=" N   MET A 111 "
    ideal  model  delta    sigma   weight residual
    1.327  1.392 -0.065 1.71e-02 3.42e+03 1.44e+01
  bond pdb=" N   THR B 432 "
       pdb=" CA  THR B 432 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.27e-02 6.20e+03 9.24e+00
  bond pdb=" N   VAL B 433 "
       pdb=" CA  VAL B 433 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.24e-02 6.50e+03 9.02e+00
  bond pdb=" N   ARG B  61 "
       pdb=" CA  ARG B  61 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.00e-02 1.00e+04 8.96e+00
  bond pdb=" N   ILE A 463 "
       pdb=" CA  ILE A 463 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.40e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 11759
        2.85 -     5.71: 297
        5.71 -     8.56: 29
        8.56 -    11.41: 6
       11.41 -    14.26: 1
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" N   ASP B 431 "
        pdb=" CA  ASP B 431 "
        pdb=" C   ASP B 431 "
      ideal   model   delta    sigma   weight residual
     109.52   99.24   10.28 1.55e+00 4.16e-01 4.40e+01
  angle pdb=" CA  ARG A 493 "
        pdb=" C   ARG A 493 "
        pdb=" O   ARG A 493 "
      ideal   model   delta    sigma   weight residual
     121.40  115.69    5.71 1.11e+00 8.12e-01 2.65e+01
  angle pdb=" N   PRO A 357 "
        pdb=" CA  PRO A 357 "
        pdb=" C   PRO A 357 "
      ideal   model   delta    sigma   weight residual
     111.14  103.45    7.69 1.56e+00 4.11e-01 2.43e+01
  angle pdb=" CA  GLU B 514 "
        pdb=" CB  GLU B 514 "
        pdb=" CG  GLU B 514 "
      ideal   model   delta    sigma   weight residual
     114.10  123.67   -9.57 2.00e+00 2.50e-01 2.29e+01
  angle pdb=" CB  MET B  44 "
        pdb=" CG  MET B  44 "
        pdb=" SD  MET B  44 "
      ideal   model   delta    sigma   weight residual
     112.70  126.96  -14.26 3.00e+00 1.11e-01 2.26e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 4690
       17.80 -    35.60: 590
       35.60 -    53.40: 145
       53.40 -    71.19: 22
       71.19 -    88.99: 7
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  GLN B 418 "
           pdb=" C   GLN B 418 "
           pdb=" N   VAL B 419 "
           pdb=" CA  VAL B 419 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.71  -23.29     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  ARG B 416 "
           pdb=" C   ARG B 416 "
           pdb=" N   ASN B 417 "
           pdb=" CA  ASN B 417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.26   22.74     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  THR B 320 "
           pdb=" C   THR B 320 "
           pdb=" N   ILE B 321 "
           pdb=" CA  ILE B 321 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.81   21.19     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1126
       0.055 -    0.111: 256
       0.111 -    0.166: 40
       0.166 -    0.221: 9
       0.221 -    0.277: 9
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  ASP B 431 "
            pdb=" N   ASP B 431 "
            pdb=" C   ASP B 431 "
            pdb=" CB  ASP B 431 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" CA  ARG A 493 "
            pdb=" N   ARG A 493 "
            pdb=" C   ARG A 493 "
            pdb=" CB  ARG A 493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CA  ILE A 463 "
            pdb=" N   ILE A 463 "
            pdb=" C   ILE A 463 "
            pdb=" CB  ILE A 463 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.66e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 492 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.21e+00
        pdb=" C   ALA A 492 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ALA A 492 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ARG A 493 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 514 "   -0.013 2.00e-02 2.50e+03   2.50e-02 6.27e+00
        pdb=" C   GLU B 514 "    0.043 2.00e-02 2.50e+03
        pdb=" O   GLU B 514 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   SER B 515 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 127 "   -0.197 9.50e-02 1.11e+02   8.88e-02 5.55e+00
        pdb=" NE  ARG B 127 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 127 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 127 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 127 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 1007
        2.74 -     3.28: 9856
        3.28 -     3.82: 14817
        3.82 -     4.36: 16989
        4.36 -     4.90: 27207
  Nonbonded interactions: 69876
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 458 "
            pdb=" NH2 ARG B 488 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" OD2 ASP A  53 "
            pdb=" OG1 THR A 280 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   MET A 160 "
            pdb=" N   SER A 164 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   ARG A  78 "
            pdb=" OG  SER A  82 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   LEU B 502 "
            pdb=" OG  SER B 532 "
     model   vdw
     2.257 3.040
  ... (remaining 69871 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:             3.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.890
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   8950  Z= 0.306
  Angle     :  1.037  14.264  12092  Z= 0.589
  Chirality :  0.052   0.277   1440
  Planarity :  0.006   0.089   1532
  Dihedral  : 16.479  88.993   3326
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.61 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 24.59 %
    Favored  : 74.69 %
  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: -1.42 (0.25), residues: 1134
  helix: -0.11 (0.20), residues: 660
  sheet: -1.93 (0.67), residues: 53
  loop : -2.07 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 127 
 TYR   0.013   0.001   TYR B 439 
 PHE   0.038   0.002   PHE A  13 
 TRP   0.007   0.001   TRP A  17 
 HIS   0.008   0.002   HIS B 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 ( 8950)
  covalent geometry    : angle       1.03718 (12092)
  hydrogen bonds       : bond        0.15433 (  478)
  hydrogen bonds       : angle       6.43903 ( 1404)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 205
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   54 ASP cc_start: 0.7772 (t0) cc_final: 0.7567 (t0)
REVERT: B  100 MET cc_start: 0.9028 (tpp) cc_final: 0.8751 (mmp)
REVERT: B  132 SER cc_start: 0.9215 (t) cc_final: 0.8875 (p)
REVERT: B  133 GLU cc_start: 0.7868 (mp0) cc_final: 0.7445 (mp0)
REVERT: B  236 ARG cc_start: 0.8898 (mmp-170) cc_final: 0.8622 (mmp-170)
REVERT: A   98 MET cc_start: 0.8296 (tmm) cc_final: 0.7639 (tmm)
REVERT: A  126 SER cc_start: 0.9404 (m) cc_final: 0.9200 (p)
  outliers start: 7
  outliers final: 2
  residues processed: 207
  average time/residue: 0.0653
  time to fit residues: 19.4727
Evaluate side-chains
  185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 183
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 ASN
** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 HIS
A 436 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.112111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.089234 restraints weight = 30582.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.091995 restraints weight = 20628.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.094058 restraints weight = 15267.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.095617 restraints weight = 12095.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.096670 restraints weight = 10042.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8950  Z= 0.146
  Angle     :  0.657   8.234  12092  Z= 0.346
  Chirality :  0.044   0.220   1440
  Planarity :  0.005   0.050   1532
  Dihedral  :  5.278  23.454   1238
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.03 %
    Favored  : 95.76 %
  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: -0.90 (0.25), residues: 1134
  helix:  0.30 (0.20), residues: 666
  sheet: -0.86 (0.71), residues: 54
  loop : -2.01 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 360 
 TYR   0.016   0.001   TYR B  87 
 PHE   0.016   0.002   PHE A 429 
 TRP   0.015   0.002   TRP A  91 
 HIS   0.005   0.001   HIS B 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8950)
  covalent geometry    : angle       0.65745 (12092)
  hydrogen bonds       : bond        0.04545 (  478)
  hydrogen bonds       : angle       4.97114 ( 1404)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 214
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 MET cc_start: 0.8972 (tmm) cc_final: 0.8736 (tmm)
REVERT: B   45 LEU cc_start: 0.9480 (mt) cc_final: 0.9277 (mt)
REVERT: B   47 LEU cc_start: 0.9162 (mt) cc_final: 0.8902 (mt)
REVERT: B  132 SER cc_start: 0.9411 (t) cc_final: 0.9010 (p)
REVERT: B  133 GLU cc_start: 0.7987 (mp0) cc_final: 0.7540 (mp0)
REVERT: B  312 MET cc_start: 0.5408 (tpp) cc_final: 0.5069 (tpp)
REVERT: B  430 ASN cc_start: 0.8017 (p0) cc_final: 0.7746 (p0)
REVERT: B  456 MET cc_start: 0.9056 (mpp) cc_final: 0.8745 (mpp)
REVERT: A   44 MET cc_start: 0.8949 (tmm) cc_final: 0.8523 (tmm)
REVERT: A   45 LEU cc_start: 0.9426 (mt) cc_final: 0.9128 (mt)
REVERT: A  126 SER cc_start: 0.9389 (m) cc_final: 0.9099 (p)
REVERT: A  144 ILE cc_start: 0.9348 (pt) cc_final: 0.8918 (pt)
REVERT: A  219 ILE cc_start: 0.9286 (mm) cc_final: 0.9023 (mm)
REVERT: A  229 ARG cc_start: 0.8604 (tpp80) cc_final: 0.8295 (ttm170)
REVERT: A  449 GLN cc_start: 0.9365 (mp10) cc_final: 0.9118 (mp10)
REVERT: A  451 GLU cc_start: 0.8835 (pt0) cc_final: 0.8255 (pp20)
  outliers start: 2
  outliers final: 0
  residues processed: 216
  average time/residue: 0.0881
  time to fit residues: 26.8841
Evaluate side-chains
  178 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 32 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   chunk 73 optimal weight:    0.1980
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 55 optimal weight:   30.0000
   chunk 38 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN
** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.112840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.089631 restraints weight = 30438.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.092369 restraints weight = 20727.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.094409 restraints weight = 15476.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.095788 restraints weight = 12308.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.097003 restraints weight = 10370.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8950  Z= 0.126
  Angle     :  0.659  12.930  12092  Z= 0.336
  Chirality :  0.043   0.218   1440
  Planarity :  0.005   0.053   1532
  Dihedral  :  5.155  23.105   1238
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.10 %
    Favored  : 96.80 %
  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: -0.77 (0.25), residues: 1134
  helix:  0.40 (0.20), residues: 663
  sheet: -0.54 (0.79), residues: 47
  loop : -1.95 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 493 
 TYR   0.014   0.001   TYR A 572 
 PHE   0.010   0.001   PHE A 220 
 TRP   0.018   0.001   TRP A  91 
 HIS   0.005   0.001   HIS B 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8950)
  covalent geometry    : angle       0.65857 (12092)
  hydrogen bonds       : bond        0.04188 (  478)
  hydrogen bonds       : angle       4.79570 ( 1404)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 217
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 MET cc_start: 0.8920 (tmm) cc_final: 0.8697 (tmm)
REVERT: B   45 LEU cc_start: 0.9452 (mt) cc_final: 0.9184 (mt)
REVERT: B   47 LEU cc_start: 0.9123 (mt) cc_final: 0.8867 (mt)
REVERT: B  132 SER cc_start: 0.9437 (t) cc_final: 0.9031 (p)
REVERT: B  133 GLU cc_start: 0.8063 (mp0) cc_final: 0.7452 (mp0)
REVERT: B  248 SER cc_start: 0.9545 (t) cc_final: 0.9337 (p)
REVERT: B  257 LEU cc_start: 0.9118 (tp) cc_final: 0.8775 (mt)
REVERT: B  388 LEU cc_start: 0.8163 (mm) cc_final: 0.7735 (mm)
REVERT: B  430 ASN cc_start: 0.7983 (p0) cc_final: 0.7743 (p0)
REVERT: B  456 MET cc_start: 0.9131 (mpp) cc_final: 0.8809 (mmm)
REVERT: A   44 MET cc_start: 0.8924 (tmm) cc_final: 0.8468 (tmm)
REVERT: A   45 LEU cc_start: 0.9439 (mt) cc_final: 0.9117 (mt)
REVERT: A  126 SER cc_start: 0.9427 (m) cc_final: 0.9160 (p)
REVERT: A  219 ILE cc_start: 0.9232 (mm) cc_final: 0.9014 (mm)
REVERT: A  229 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8184 (ttm170)
REVERT: A  248 SER cc_start: 0.9566 (t) cc_final: 0.9300 (p)
REVERT: A  451 GLU cc_start: 0.8863 (pt0) cc_final: 0.8267 (pp20)
  outliers start: 1
  outliers final: 0
  residues processed: 218
  average time/residue: 0.0952
  time to fit residues: 29.0164
Evaluate side-chains
  175 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 71 optimal weight:    0.5980
   chunk 66 optimal weight:    0.4980
   chunk 36 optimal weight:    8.9990
   chunk 81 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0070
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 134 GLN
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.114338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.090789 restraints weight = 31709.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.093522 restraints weight = 21958.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.095510 restraints weight = 16587.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.097093 restraints weight = 13349.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.098250 restraints weight = 11214.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8950  Z= 0.120
  Angle     :  0.645  10.169  12092  Z= 0.329
  Chirality :  0.043   0.263   1440
  Planarity :  0.004   0.043   1532
  Dihedral  :  5.037  21.829   1238
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  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: -0.69 (0.26), residues: 1134
  helix:  0.47 (0.20), residues: 665
  sheet: -0.08 (0.76), residues: 52
  loop : -2.01 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 441 
 TYR   0.021   0.001   TYR B 393 
 PHE   0.012   0.001   PHE A 220 
 TRP   0.011   0.001   TRP A  91 
 HIS   0.008   0.001   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8950)
  covalent geometry    : angle       0.64455 (12092)
  hydrogen bonds       : bond        0.03954 (  478)
  hydrogen bonds       : angle       4.66883 ( 1404)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 LEU cc_start: 0.9432 (mt) cc_final: 0.9205 (mt)
REVERT: B   47 LEU cc_start: 0.9071 (mt) cc_final: 0.8746 (mt)
REVERT: B  132 SER cc_start: 0.9469 (t) cc_final: 0.9170 (p)
REVERT: B  133 GLU cc_start: 0.8124 (mp0) cc_final: 0.7665 (mp0)
REVERT: B  430 ASN cc_start: 0.8035 (p0) cc_final: 0.7796 (p0)
REVERT: B  431 ASP cc_start: 0.7102 (t0) cc_final: 0.6873 (t0)
REVERT: B  456 MET cc_start: 0.9178 (mpp) cc_final: 0.8852 (mmm)
REVERT: A   44 MET cc_start: 0.8937 (tmm) cc_final: 0.8585 (tmm)
REVERT: A   45 LEU cc_start: 0.9442 (mt) cc_final: 0.9115 (mt)
REVERT: A  126 SER cc_start: 0.9462 (m) cc_final: 0.9215 (p)
REVERT: A  219 ILE cc_start: 0.9274 (mm) cc_final: 0.9060 (mm)
REVERT: A  229 ARG cc_start: 0.8587 (tpp80) cc_final: 0.8279 (ttm170)
REVERT: A  248 SER cc_start: 0.9555 (t) cc_final: 0.9311 (p)
REVERT: A  449 GLN cc_start: 0.9408 (mt0) cc_final: 0.9015 (mp10)
REVERT: A  488 ARG cc_start: 0.8659 (ttt180) cc_final: 0.8459 (ttt180)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 0.0880
  time to fit residues: 27.9494
Evaluate side-chains
  176 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 111 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 16 optimal weight:   10.0000
   chunk 81 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN
B 424 GLN
B 436 ASN
B 477 ASN
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 309 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.106162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.083047 restraints weight = 32812.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.085547 restraints weight = 22904.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.087487 restraints weight = 17469.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.088796 restraints weight = 14080.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.089970 restraints weight = 11981.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8950  Z= 0.202
  Angle     :  0.712   9.642  12092  Z= 0.377
  Chirality :  0.046   0.241   1440
  Planarity :  0.005   0.041   1532
  Dihedral  :  5.472  26.282   1238
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 18.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.79 %
    Favored  : 96.90 %
  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: -0.88 (0.25), residues: 1134
  helix:  0.27 (0.20), residues: 671
  sheet: -0.57 (0.72), residues: 50
  loop : -1.98 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 486 
 TYR   0.012   0.002   TYR B  87 
 PHE   0.023   0.002   PHE B 319 
 TRP   0.014   0.001   TRP A  91 
 HIS   0.007   0.002   HIS B 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8950)
  covalent geometry    : angle       0.71234 (12092)
  hydrogen bonds       : bond        0.04433 (  478)
  hydrogen bonds       : angle       4.97938 ( 1404)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 211
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 MET cc_start: 0.8935 (tmm) cc_final: 0.8565 (tmm)
REVERT: B   47 LEU cc_start: 0.9188 (mt) cc_final: 0.8957 (mt)
REVERT: B   98 MET cc_start: 0.8801 (tpt) cc_final: 0.8550 (tpp)
REVERT: B  109 MET cc_start: 0.8913 (mmp) cc_final: 0.8699 (mmp)
REVERT: B  132 SER cc_start: 0.9589 (t) cc_final: 0.9229 (p)
REVERT: B  133 GLU cc_start: 0.8214 (mp0) cc_final: 0.7718 (mp0)
REVERT: B  229 ARG cc_start: 0.8768 (ttm170) cc_final: 0.8350 (ttm170)
REVERT: B  456 MET cc_start: 0.9211 (mpp) cc_final: 0.8892 (mpp)
REVERT: B  460 MET cc_start: 0.8023 (mmt) cc_final: 0.7518 (mmp)
REVERT: A   44 MET cc_start: 0.9062 (tmm) cc_final: 0.8675 (tmm)
REVERT: A   45 LEU cc_start: 0.9460 (mt) cc_final: 0.9078 (mt)
REVERT: A  126 SER cc_start: 0.9498 (m) cc_final: 0.9297 (p)
REVERT: A  219 ILE cc_start: 0.9351 (mm) cc_final: 0.9129 (mm)
REVERT: A  229 ARG cc_start: 0.8897 (tpp80) cc_final: 0.8663 (tpp80)
REVERT: A  248 SER cc_start: 0.9608 (t) cc_final: 0.9378 (p)
REVERT: A  359 LEU cc_start: 0.7692 (mp) cc_final: 0.7397 (pp)
REVERT: A  449 GLN cc_start: 0.9396 (mt0) cc_final: 0.9053 (mp10)
  outliers start: 3
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0770
  time to fit residues: 23.3452
Evaluate side-chains
  169 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    0.0980
   chunk 95 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 108 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 79 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN
B 436 ASN
B 527 GLN
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 240 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.111663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.088358 restraints weight = 32084.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.090975 restraints weight = 22418.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.092815 restraints weight = 17056.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.094339 restraints weight = 13904.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.095398 restraints weight = 11759.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8950  Z= 0.127
  Angle     :  0.661   9.211  12092  Z= 0.339
  Chirality :  0.043   0.229   1440
  Planarity :  0.004   0.043   1532
  Dihedral  :  5.104  24.415   1238
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  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: -0.65 (0.25), residues: 1134
  helix:  0.47 (0.20), residues: 664
  sheet:  0.35 (0.85), residues: 40
  loop : -1.94 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 441 
 TYR   0.011   0.001   TYR A 439 
 PHE   0.018   0.001   PHE B 319 
 TRP   0.016   0.002   TRP B  91 
 HIS   0.006   0.001   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8950)
  covalent geometry    : angle       0.66099 (12092)
  hydrogen bonds       : bond        0.03925 (  478)
  hydrogen bonds       : angle       4.66028 ( 1404)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 MET cc_start: 0.8828 (tmm) cc_final: 0.8587 (tmm)
REVERT: B   45 LEU cc_start: 0.9458 (mt) cc_final: 0.9202 (mt)
REVERT: B   47 LEU cc_start: 0.9082 (mt) cc_final: 0.8750 (mt)
REVERT: B   98 MET cc_start: 0.8640 (tpt) cc_final: 0.6827 (tpp)
REVERT: B  132 SER cc_start: 0.9519 (t) cc_final: 0.9166 (p)
REVERT: B  133 GLU cc_start: 0.8167 (mp0) cc_final: 0.7621 (mp0)
REVERT: B  229 ARG cc_start: 0.8680 (ttm170) cc_final: 0.8203 (ttm170)
REVERT: B  295 MET cc_start: 0.7652 (mtp) cc_final: 0.7065 (mmm)
REVERT: B  316 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8962 (tp-100)
REVERT: B  430 ASN cc_start: 0.8076 (p0) cc_final: 0.7429 (p0)
REVERT: B  431 ASP cc_start: 0.7630 (t0) cc_final: 0.7151 (t0)
REVERT: B  456 MET cc_start: 0.9240 (mpp) cc_final: 0.8934 (mmm)
REVERT: B  460 MET cc_start: 0.7456 (mmt) cc_final: 0.7017 (mmp)
REVERT: A   44 MET cc_start: 0.8980 (tmm) cc_final: 0.8616 (tmm)
REVERT: A   45 LEU cc_start: 0.9422 (mt) cc_final: 0.9073 (mt)
REVERT: A  126 SER cc_start: 0.9506 (m) cc_final: 0.9281 (p)
REVERT: A  219 ILE cc_start: 0.9270 (mm) cc_final: 0.9054 (mm)
REVERT: A  229 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8388 (ttm170)
REVERT: A  248 SER cc_start: 0.9605 (t) cc_final: 0.9378 (p)
REVERT: A  359 LEU cc_start: 0.7480 (mp) cc_final: 0.7272 (pt)
REVERT: A  449 GLN cc_start: 0.9380 (mt0) cc_final: 0.8995 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0801
  time to fit residues: 25.5211
Evaluate side-chains
  177 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 57 optimal weight:    0.3980
   chunk 104 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0980
   chunk 88 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 93 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 134 GLN
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.111284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.088081 restraints weight = 30843.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.090814 restraints weight = 20926.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.092882 restraints weight = 15577.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.094199 restraints weight = 12327.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.095482 restraints weight = 10471.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.3950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8950  Z= 0.126
  Angle     :  0.676   9.939  12092  Z= 0.346
  Chirality :  0.044   0.285   1440
  Planarity :  0.004   0.040   1532
  Dihedral  :  5.073  24.006   1238
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  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: -0.58 (0.26), residues: 1134
  helix:  0.53 (0.20), residues: 667
  sheet:  0.44 (0.86), residues: 40
  loop : -1.93 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 102 
 TYR   0.015   0.001   TYR B 439 
 PHE   0.016   0.001   PHE A 230 
 TRP   0.013   0.001   TRP B  91 
 HIS   0.006   0.001   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8950)
  covalent geometry    : angle       0.67574 (12092)
  hydrogen bonds       : bond        0.03786 (  478)
  hydrogen bonds       : angle       4.63359 ( 1404)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 LEU cc_start: 0.9435 (mt) cc_final: 0.9144 (mt)
REVERT: B   47 LEU cc_start: 0.9049 (mt) cc_final: 0.8729 (mt)
REVERT: B   98 MET cc_start: 0.8895 (tpt) cc_final: 0.8520 (tpp)
REVERT: B  132 SER cc_start: 0.9483 (t) cc_final: 0.9152 (p)
REVERT: B  133 GLU cc_start: 0.8276 (mp0) cc_final: 0.7677 (mp0)
REVERT: B  229 ARG cc_start: 0.8786 (ttm170) cc_final: 0.8287 (ttm170)
REVERT: B  430 ASN cc_start: 0.7952 (p0) cc_final: 0.7692 (p0)
REVERT: B  456 MET cc_start: 0.9245 (mpp) cc_final: 0.8933 (mmm)
REVERT: B  460 MET cc_start: 0.7578 (mmt) cc_final: 0.7096 (mmp)
REVERT: A   44 MET cc_start: 0.9041 (tmm) cc_final: 0.8639 (tmm)
REVERT: A  126 SER cc_start: 0.9513 (m) cc_final: 0.9300 (p)
REVERT: A  157 PHE cc_start: 0.8576 (t80) cc_final: 0.8331 (t80)
REVERT: A  229 ARG cc_start: 0.8810 (tpp80) cc_final: 0.8579 (tpp80)
REVERT: A  248 SER cc_start: 0.9582 (t) cc_final: 0.9356 (p)
REVERT: A  441 ARG cc_start: 0.8324 (ptp90) cc_final: 0.8046 (ptp90)
REVERT: A  449 GLN cc_start: 0.9382 (mt0) cc_final: 0.8991 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.0801
  time to fit residues: 25.7077
Evaluate side-chains
  185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 88 optimal weight:    0.0060
   chunk 33 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 4 optimal weight:    9.9990
   chunk 28 optimal weight:    0.0980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 134 GLN
B 485 GLN
** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.112361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.089300 restraints weight = 30627.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.092082 restraints weight = 20839.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.094130 restraints weight = 15519.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.095673 restraints weight = 12272.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.096705 restraints weight = 10197.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.4172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8950  Z= 0.122
  Angle     :  0.673   8.921  12092  Z= 0.342
  Chirality :  0.043   0.220   1440
  Planarity :  0.004   0.039   1532
  Dihedral  :  4.947  23.095   1238
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  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: -0.54 (0.26), residues: 1134
  helix:  0.54 (0.20), residues: 667
  sheet:  0.51 (0.87), residues: 40
  loop : -1.90 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 102 
 TYR   0.010   0.001   TYR B  87 
 PHE   0.018   0.001   PHE B  23 
 TRP   0.012   0.001   TRP B  91 
 HIS   0.006   0.001   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8950)
  covalent geometry    : angle       0.67335 (12092)
  hydrogen bonds       : bond        0.03764 (  478)
  hydrogen bonds       : angle       4.56373 ( 1404)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 LEU cc_start: 0.9402 (mt) cc_final: 0.9138 (mt)
REVERT: B   47 LEU cc_start: 0.9018 (mt) cc_final: 0.8604 (mt)
REVERT: B   98 MET cc_start: 0.8870 (tpt) cc_final: 0.8512 (tpp)
REVERT: B  132 SER cc_start: 0.9484 (t) cc_final: 0.9081 (p)
REVERT: B  133 GLU cc_start: 0.8231 (mp0) cc_final: 0.7687 (mp0)
REVERT: B  257 LEU cc_start: 0.9070 (mt) cc_final: 0.8745 (mt)
REVERT: B  430 ASN cc_start: 0.7883 (p0) cc_final: 0.7637 (p0)
REVERT: B  456 MET cc_start: 0.9286 (mpp) cc_final: 0.8975 (mmm)
REVERT: B  460 MET cc_start: 0.7486 (mmt) cc_final: 0.7030 (mmp)
REVERT: A   44 MET cc_start: 0.9020 (tmm) cc_final: 0.8640 (tmm)
REVERT: A   45 LEU cc_start: 0.9428 (mt) cc_final: 0.9108 (mt)
REVERT: A  126 SER cc_start: 0.9509 (m) cc_final: 0.9284 (p)
REVERT: A  157 PHE cc_start: 0.8533 (t80) cc_final: 0.8296 (t80)
REVERT: A  229 ARG cc_start: 0.8785 (tpp80) cc_final: 0.8570 (tpp80)
REVERT: A  248 SER cc_start: 0.9564 (t) cc_final: 0.9338 (p)
REVERT: A  441 ARG cc_start: 0.8249 (ptp90) cc_final: 0.8042 (ptp90)
REVERT: A  449 GLN cc_start: 0.9364 (mt0) cc_final: 0.8995 (mp10)
REVERT: A  466 MET cc_start: 0.2467 (mmp) cc_final: 0.2245 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.0837
  time to fit residues: 26.2696
Evaluate side-chains
  186 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0170
   chunk 57 optimal weight:    0.0270
   chunk 33 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 134 GLN
** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  37 ASN
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.113101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.090102 restraints weight = 30633.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.092847 restraints weight = 21216.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.094830 restraints weight = 15941.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.096315 restraints weight = 12748.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.097462 restraints weight = 10681.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.4307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8950  Z= 0.123
  Angle     :  0.693   8.644  12092  Z= 0.348
  Chirality :  0.043   0.231   1440
  Planarity :  0.004   0.039   1532
  Dihedral  :  4.880  23.147   1238
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  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: -0.50 (0.26), residues: 1134
  helix:  0.59 (0.20), residues: 661
  sheet:  0.52 (0.88), residues: 40
  loop : -1.87 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 102 
 TYR   0.009   0.001   TYR B 393 
 PHE   0.016   0.001   PHE A 230 
 TRP   0.013   0.001   TRP B  91 
 HIS   0.005   0.001   HIS B 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8950)
  covalent geometry    : angle       0.69287 (12092)
  hydrogen bonds       : bond        0.03743 (  478)
  hydrogen bonds       : angle       4.54960 ( 1404)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 LEU cc_start: 0.9357 (mt) cc_final: 0.9087 (mt)
REVERT: B   47 LEU cc_start: 0.8922 (mt) cc_final: 0.8610 (mt)
REVERT: B   98 MET cc_start: 0.8855 (tpt) cc_final: 0.8451 (tpp)
REVERT: B  108 MET cc_start: 0.9220 (mpp) cc_final: 0.9016 (mtm)
REVERT: B  132 SER cc_start: 0.9431 (t) cc_final: 0.9096 (p)
REVERT: B  133 GLU cc_start: 0.8238 (mp0) cc_final: 0.7678 (mp0)
REVERT: B  257 LEU cc_start: 0.9077 (mt) cc_final: 0.8794 (mt)
REVERT: B  312 MET cc_start: 0.5568 (tpp) cc_final: 0.5071 (tpp)
REVERT: B  456 MET cc_start: 0.9214 (mpp) cc_final: 0.8804 (mpp)
REVERT: B  460 MET cc_start: 0.7512 (mmt) cc_final: 0.7105 (mmp)
REVERT: B  474 ILE cc_start: 0.8151 (mp) cc_final: 0.7889 (mm)
REVERT: A   44 MET cc_start: 0.9006 (tmm) cc_final: 0.8613 (tmm)
REVERT: A  126 SER cc_start: 0.9498 (m) cc_final: 0.9284 (p)
REVERT: A  157 PHE cc_start: 0.8498 (t80) cc_final: 0.8067 (t80)
REVERT: A  248 SER cc_start: 0.9547 (t) cc_final: 0.9329 (p)
REVERT: A  441 ARG cc_start: 0.8292 (ptp90) cc_final: 0.8071 (ptp90)
REVERT: A  449 GLN cc_start: 0.9347 (mt0) cc_final: 0.8987 (mp10)
REVERT: A  466 MET cc_start: 0.2134 (mmp) cc_final: 0.1908 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.0769
  time to fit residues: 24.1583
Evaluate side-chains
  182 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 47 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 92 optimal weight:    5.9990
   chunk 108 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 109 optimal weight:    5.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.109457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.086525 restraints weight = 30804.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.089215 restraints weight = 20845.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.091179 restraints weight = 15474.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.092605 restraints weight = 12288.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.093755 restraints weight = 10296.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.4412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8950  Z= 0.142
  Angle     :  0.695   8.778  12092  Z= 0.354
  Chirality :  0.044   0.234   1440
  Planarity :  0.004   0.038   1532
  Dihedral  :  4.962  23.665   1238
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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: -0.52 (0.26), residues: 1134
  helix:  0.54 (0.20), residues: 662
  sheet:  0.39 (0.89), residues: 40
  loop : -1.81 (0.32), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 102 
 TYR   0.012   0.001   TYR B 439 
 PHE   0.019   0.002   PHE B  23 
 TRP   0.014   0.001   TRP B  91 
 HIS   0.006   0.001   HIS B 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8950)
  covalent geometry    : angle       0.69535 (12092)
  hydrogen bonds       : bond        0.03848 (  478)
  hydrogen bonds       : angle       4.64499 ( 1404)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 MET cc_start: 0.8761 (tmm) cc_final: 0.8529 (tmm)
REVERT: B   45 LEU cc_start: 0.9409 (mt) cc_final: 0.8947 (mt)
REVERT: B   47 LEU cc_start: 0.8949 (mt) cc_final: 0.8659 (mt)
REVERT: B   98 MET cc_start: 0.8973 (tpt) cc_final: 0.8724 (tpp)
REVERT: B  133 GLU cc_start: 0.8254 (mp0) cc_final: 0.7931 (mp0)
REVERT: B  257 LEU cc_start: 0.9024 (mt) cc_final: 0.8733 (mt)
REVERT: B  430 ASN cc_start: 0.7948 (p0) cc_final: 0.7531 (p0)
REVERT: B  456 MET cc_start: 0.9258 (mpp) cc_final: 0.8928 (mpp)
REVERT: B  460 MET cc_start: 0.7723 (mmt) cc_final: 0.7303 (mmp)
REVERT: B  474 ILE cc_start: 0.8209 (mp) cc_final: 0.7905 (mm)
REVERT: A   37 ASN cc_start: 0.9269 (t0) cc_final: 0.9051 (t0)
REVERT: A   44 MET cc_start: 0.9056 (tmm) cc_final: 0.8667 (tmm)
REVERT: A   45 LEU cc_start: 0.9430 (mt) cc_final: 0.9114 (mt)
REVERT: A  157 PHE cc_start: 0.8611 (t80) cc_final: 0.8366 (t80)
REVERT: A  219 ILE cc_start: 0.9351 (mm) cc_final: 0.9076 (mm)
REVERT: A  248 SER cc_start: 0.9566 (t) cc_final: 0.9342 (p)
REVERT: A  449 GLN cc_start: 0.9360 (mt0) cc_final: 0.9011 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.0795
  time to fit residues: 24.5608
Evaluate side-chains
  170 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 104 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0020
   overall best weight:    0.8590

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

Flipped N/Q/H residues before XYZ refinement:
B 134 GLN
** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 527 GLN
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.110587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.087596 restraints weight = 30461.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.090237 restraints weight = 20762.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.092261 restraints weight = 15574.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.093764 restraints weight = 12382.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.094697 restraints weight = 10316.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.4513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8950  Z= 0.131
  Angle     :  0.713  11.068  12092  Z= 0.359
  Chirality :  0.044   0.320   1440
  Planarity :  0.004   0.038   1532
  Dihedral  :  4.956  23.209   1238
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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: -0.49 (0.26), residues: 1134
  helix:  0.56 (0.20), residues: 661
  sheet:  0.49 (0.91), residues: 40
  loop : -1.81 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 102 
 TYR   0.009   0.001   TYR B  87 
 PHE   0.017   0.001   PHE A 230 
 TRP   0.013   0.001   TRP B  91 
 HIS   0.006   0.001   HIS B 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8950)
  covalent geometry    : angle       0.71269 (12092)
  hydrogen bonds       : bond        0.03834 (  478)
  hydrogen bonds       : angle       4.63550 ( 1404)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1679.95 seconds
wall clock time: 29 minutes 48.09 seconds (1788.09 seconds total)