Starting phenix.real_space_refine
on Wed Mar  4 04:55:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ele_31182/03_2026/7ele_31182.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ele_31182/03_2026/7ele_31182.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ele_31182/03_2026/7ele_31182.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ele_31182/03_2026/7ele_31182.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ele_31182/03_2026/7ele_31182.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ele_31182/03_2026/7ele_31182.map"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     P      83      5.49       5
     S      60      5.16       5
     C    6512      2.51       5
     N    1851      2.21       5
     O    2227      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10733
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8976
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1137, 8976
          Classifications: {'peptide': 1137}
          Link IDs: {'PTRANS': 38, 'TRANS': 1098}
          Chain breaks: 12
    Chain: "G"
      Number of atoms: 1757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 1757
          Classifications: {'RNA': 83}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 39, 'rna3p_pyr': 42}
          Link IDs: {'rna2p': 1, 'rna3p': 81}
          Chain breaks: 3
  Time building chain proxies: 2.30, per 1000 atoms: 0.21
  Number of scatterers: 10733
  At special positions: 0
  Unit cell: (161.226, 129.792, 93.288, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P      83     15.00
     O    2227      8.00
     N    1851      7.00
     C    6512      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: 0.90
  Conformation dependent library (CDL) restraints added in 458.9 milliseconds
  

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 5 sheets defined
      54.4% alpha, 6.6% beta
      35 base pairs and 61 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 250 through 263
      removed outlier: 3.828A  pdb=" N   LEU A 254 " --> pdb=" O   ARG A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 289
    Processing helix  chain 'A' and resid 305 through 319
    Processing helix  chain 'A' and resid 335 through 348
      removed outlier: 4.055A  pdb=" N   ARG A 339 " --> pdb=" O   PHE A 335 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   GLU A 346 " --> pdb=" O   GLN A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 363
    Processing helix  chain 'A' and resid 364 through 366
      No H-bonds generated for 'chain 'A' and resid 364 through 366'
    Processing helix  chain 'A' and resid 368 through 372
      removed outlier: 3.739A  pdb=" N   ILE A 372 " --> pdb=" O   MET A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 383
    Processing helix  chain 'A' and resid 387 through 396
      removed outlier: 3.887A  pdb=" N   LEU A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLU A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 438
    Processing helix  chain 'A' and resid 473 through 493
      removed outlier: 3.912A  pdb=" N   THR A 477 " --> pdb=" O   SER A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 567
      removed outlier: 3.612A  pdb=" N   GLY A 545 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   GLN A 546 " --> pdb=" O   ALA A 542 " (cutoff:3.500A)
      removed outlier: 9.610A  pdb=" N   TRP A 547 " --> pdb=" O   GLU A 543 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   CYS A 548 " --> pdb=" O   LEU A 544 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ALA A 549 " --> pdb=" O   GLY A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 593
      removed outlier: 3.752A  pdb=" N   GLU A 592 " --> pdb=" O   CYS A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 659
    Processing helix  chain 'A' and resid 673 through 687
      Proline residue:  A 681  - end of helix
    Processing helix  chain 'A' and resid 708 through 721
    Processing helix  chain 'A' and resid 721 through 728
    Processing helix  chain 'A' and resid 753 through 763
    Processing helix  chain 'A' and resid 781 through 801
    Processing helix  chain 'A' and resid 823 through 826
      removed outlier: 3.956A  pdb=" N   TYR A 826 " --> pdb=" O   GLY A 823 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 823 through 826'
    Processing helix  chain 'A' and resid 827 through 849
      removed outlier: 3.810A  pdb=" N   THR A 831 " --> pdb=" O   LYS A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 918
    Processing helix  chain 'A' and resid 1049 through 1066
    Processing helix  chain 'A' and resid 1103 through 1113
    Processing helix  chain 'A' and resid 1254 through 1264
    Processing helix  chain 'A' and resid 1301 through 1307
      removed outlier: 4.085A  pdb=" N   VAL A1307 " --> pdb=" O   LYS A1303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1320 through 1348
      Proline residue:  A1331  - end of helix
      removed outlier: 3.565A  pdb=" N   ASN A1348 " --> pdb=" O   VAL A1344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1358 through 1364
      removed outlier: 3.508A  pdb=" N   THR A1364 " --> pdb=" O   LEU A1360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1374 through 1397
    Processing helix  chain 'A' and resid 1401 through 1413
    Processing helix  chain 'A' and resid 1414 through 1426
      removed outlier: 3.589A  pdb=" N   LEU A1418 " --> pdb=" O   SER A1414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1427 through 1430
    Processing helix  chain 'A' and resid 1501 through 1517
      removed outlier: 3.753A  pdb=" N   GLY A1517 " --> pdb=" O   TYR A1513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1518 through 1530
      removed outlier: 3.740A  pdb=" N   ALA A1522 " --> pdb=" O   GLY A1518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1559 through 1566
    Processing helix  chain 'A' and resid 1572 through 1581
      removed outlier: 3.696A  pdb=" N   LEU A1576 " --> pdb=" O   GLU A1572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1593 through 1615
    Processing helix  chain 'A' and resid 1620 through 1632
    Processing helix  chain 'A' and resid 1633 through 1645
      removed outlier: 3.548A  pdb=" N   PHE A1637 " --> pdb=" O   ASN A1633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1654 through 1668
      removed outlier: 3.628A  pdb=" N   GLU A1658 " --> pdb=" O   SER A1654 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL A1668 " --> pdb=" O   PHE A1664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1690 through 1706
    Processing helix  chain 'A' and resid 1710 through 1722
      removed outlier: 3.512A  pdb=" N   VAL A1716 " --> pdb=" O   ALA A1712 " (cutoff:3.500A)
      Proline residue:  A1719  - end of helix
    Processing helix  chain 'A' and resid 1723 through 1725
      No H-bonds generated for 'chain 'A' and resid 1723 through 1725'
    Processing helix  chain 'A' and resid 1733 through 1742
    Processing helix  chain 'A' and resid 1781 through 1794
    Processing sheet with id=AA1, first strand: chain 'A' and resid 300 through 302
      removed outlier: 5.618A  pdb=" N   VAL A 300 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   ASP A 378 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   LEU A 302 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   LEU A 375 " --> pdb=" O   PHE A 409 " (cutoff:3.500A)
      removed outlier: 8.219A  pdb=" N   MET A 411 " --> pdb=" O   LEU A 375 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LEU A 377 " --> pdb=" O   MET A 411 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   THR A 265 " --> pdb=" O   GLY A 410 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   ILE A 266 " --> pdb=" O   CYS A 443 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 463
      removed outlier: 5.835A  pdb=" N   SER A 459 " --> pdb=" O   TYR A 771 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   LEU A 773 " --> pdb=" O   SER A 459 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ILE A 461 " --> pdb=" O   LEU A 773 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   VAL A 745 " --> pdb=" O   ILE A 772 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   MET A 774 " --> pdb=" O   VAL A 745 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   ILE A 668 " --> pdb=" O   MET A 746 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ALA A 667 " --> pdb=" O   ALA A 729 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 862 through 867
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1026 through 1029
      removed outlier: 4.882A  pdb=" N   SER A 979 " --> pdb=" O   ILE A1011 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ILE A1011 " --> pdb=" O   SER A 979 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU A1086 " --> pdb=" O   LEU A1012 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1308 through 1309
      removed outlier: 6.431A  pdb=" N   LEU A1274 " --> pdb=" O   ILE A1230 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   ILE A1230 " --> pdb=" O   LEU A1274 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   LYS A1276 " --> pdb=" O   ASP A1228 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ASP A1228 " --> pdb=" O   LYS A1276 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU A1211 " --> pdb=" O   HIS A1317 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL A1315 " --> pdb=" O   GLY A1213 " (cutoff:3.500A)

    440 hydrogen bonds defined for protein.
    1296 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      81 hydrogen bonds
      142 hydrogen bond angles
      0 basepair planarities
      35 basepair parallelities
      61 stacking parallelities
  Total time for adding SS restraints: 2.74

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1869
        1.33 -     1.45: 3078
        1.45 -     1.57: 5886
        1.57 -     1.69: 162
        1.69 -     1.81: 96
  Bond restraints: 11091
  Sorted by residual:
  bond pdb=" N   ILE A 693 "
       pdb=" CA  ILE A 693 "
    ideal  model  delta    sigma   weight residual
    1.456  1.498 -0.042 1.11e-02 8.12e+03 1.45e+01
  bond pdb=" N   VAL A 728 "
       pdb=" CA  VAL A 728 "
    ideal  model  delta    sigma   weight residual
    1.459  1.503 -0.044 1.25e-02 6.40e+03 1.24e+01
  bond pdb=" N   ILE A 367 "
       pdb=" CA  ILE A 367 "
    ideal  model  delta    sigma   weight residual
    1.459  1.501 -0.042 1.25e-02 6.40e+03 1.11e+01
  bond pdb=" N   VAL A 669 "
       pdb=" CA  VAL A 669 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.17e-02 7.31e+03 1.04e+01
  bond pdb=" N   ILE A 858 "
       pdb=" CA  ILE A 858 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.17e-02 7.31e+03 1.01e+01
  ... (remaining 11086 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 14113
        2.04 -     4.07: 1096
        4.07 -     6.11: 114
        6.11 -     8.14: 28
        8.14 -    10.18: 7
  Bond angle restraints: 15358
  Sorted by residual:
  angle pdb=" N   LEU A1427 "
        pdb=" CA  LEU A1427 "
        pdb=" C   LEU A1427 "
      ideal   model   delta    sigma   weight residual
     113.19  105.76    7.43 1.19e+00 7.06e-01 3.90e+01
  angle pdb=" C4'   U G  49 "
        pdb=" C3'   U G  49 "
        pdb=" O3'   U G  49 "
      ideal   model   delta    sigma   weight residual
     113.00  121.48   -8.48 1.50e+00 4.44e-01 3.20e+01
  angle pdb=" N   GLU A 799 "
        pdb=" CA  GLU A 799 "
        pdb=" C   GLU A 799 "
      ideal   model   delta    sigma   weight residual
     112.89  106.12    6.77 1.24e+00 6.50e-01 2.98e+01
  angle pdb=" N   THR A1501 "
        pdb=" CA  THR A1501 "
        pdb=" C   THR A1501 "
      ideal   model   delta    sigma   weight residual
     113.02  106.92    6.10 1.20e+00 6.94e-01 2.58e+01
  angle pdb=" N   THR A 412 "
        pdb=" CA  THR A 412 "
        pdb=" C   THR A 412 "
      ideal   model   delta    sigma   weight residual
     113.30  106.50    6.80 1.34e+00 5.57e-01 2.57e+01
  ... (remaining 15353 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 6330
       35.91 -    71.82: 483
       71.82 -   107.73: 33
      107.73 -   143.65: 1
      143.65 -   179.56: 3
  Dihedral angle restraints: 6850
    sinusoidal: 3524
      harmonic: 3326
  Sorted by residual:
  dihedral pdb=" CA  GLN A1722 "
           pdb=" C   GLN A1722 "
           pdb=" N   PRO A1723 "
           pdb=" CA  PRO A1723 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.75  -28.25     0      5.00e+00 4.00e-02 3.19e+01
  dihedral pdb=" CA  TYR A 327 "
           pdb=" C   TYR A 327 "
           pdb=" N   CYS A 328 "
           pdb=" CA  CYS A 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.02   27.98     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  TYR A1374 "
           pdb=" C   TYR A1374 "
           pdb=" N   GLU A1375 "
           pdb=" CA  GLU A1375 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.83  -27.17     0      5.00e+00 4.00e-02 2.95e+01
  ... (remaining 6847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 1537
       0.087 -    0.173: 253
       0.173 -    0.260: 38
       0.260 -    0.346: 2
       0.346 -    0.433: 1
  Chirality restraints: 1831
  Sorted by residual:
  chirality pdb=" C3'   U G  49 "
            pdb=" C4'   U G  49 "
            pdb=" O3'   U G  49 "
            pdb=" C2'   U G  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.04   -0.43 2.00e-01 2.50e+01 4.68e+00
  chirality pdb=" C2'   G G  36 "
            pdb=" C3'   G G  36 "
            pdb=" O2'   G G  36 "
            pdb=" C1'   G G  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.43   -0.32 2.00e-01 2.50e+01 2.54e+00
  chirality pdb=" C3'   U G  25 "
            pdb=" C4'   U G  25 "
            pdb=" O3'   U G  25 "
            pdb=" C2'   U G  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.22   -0.26 2.00e-01 2.50e+01 1.70e+00
  ... (remaining 1828 not shown)

  Planarity restraints: 1638
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 663 "    0.012 2.00e-02 2.50e+03   2.54e-02 6.48e+00
        pdb=" C   ALA A 663 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ALA A 663 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ASP A 664 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 387 "   -0.041 5.00e-02 4.00e+02   6.27e-02 6.28e+00
        pdb=" N   PRO A 388 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 388 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 388 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A1426 "   -0.012 2.00e-02 2.50e+03   2.33e-02 5.43e+00
        pdb=" C   GLY A1426 "    0.040 2.00e-02 2.50e+03
        pdb=" O   GLY A1426 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A1427 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1635 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1544
        2.75 -     3.29: 11596
        3.29 -     3.82: 21135
        3.82 -     4.36: 24828
        4.36 -     4.90: 34960
  Nonbonded interactions: 94063
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 789 "
            pdb=" OG  SER A 792 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   PHE A 846 "
            pdb=" OG  SER A 849 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O2    U G  26 "
            pdb=" N2    G G  62 "
     model   vdw
     2.231 2.496
  nonbonded pdb=" O   LEU A 391 "
            pdb=" OG  SER A 394 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   LEU A1301 "
            pdb=" OG1 THR A1304 "
     model   vdw
     2.239 3.040
  ... (remaining 94058 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     12.590
  Find NCS groups from input model:        0.050
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  11091  Z= 0.457
  Angle     :  1.164  10.177  15358  Z= 0.721
  Chirality :  0.065   0.433   1831
  Planarity :  0.006   0.063   1638
  Dihedral  : 21.734 179.557   4690
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  :  9.09 %
    Favored  : 90.10 %
  Rotamer:
    Outliers :  8.44 %
    Allowed  : 13.63 %
    Favored  : 77.92 %
  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 are not related in a simple way.
  whole: -3.55 (0.21), residues: 1111
  helix: -1.87 (0.18), residues: 568
  sheet: -2.57 (0.51), residues: 75
  loop : -2.84 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1391 
 TYR   0.021   0.003   TYR A 757 
 PHE   0.022   0.003   PHE A1392 
 TRP   0.018   0.003   TRP A 336 
 HIS   0.010   0.002   HIS A 916 

Details of bonding type rmsd
  covalent geometry    : bond        0.00715 (11091)
  covalent geometry    : angle       1.16387 (15358)
  hydrogen bonds       : bond        0.14768 (  521)
  hydrogen bonds       : angle       8.00343 ( 1438)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 122
  time to evaluate  : 0.291 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  312 GLN cc_start: 0.9818 (mm-40) cc_final: 0.9533 (tp40)
REVERT: A  331 MET cc_start: 0.7068 (mtp) cc_final: 0.6798 (mtm)
REVERT: A  352 VAL cc_start: 0.9594 (t) cc_final: 0.9234 (m)
REVERT: A  393 MET cc_start: 0.9478 (tpt) cc_final: 0.9058 (tpp)
REVERT: A  397 TYR cc_start: 0.9695 (t80) cc_final: 0.9456 (t80)
REVERT: A  670 PHE cc_start: 0.9605 (m-80) cc_final: 0.9271 (m-80)
REVERT: A  691 SER cc_start: 0.9230 (OUTLIER) cc_final: 0.9010 (p)
REVERT: A  746 MET cc_start: 0.9629 (OUTLIER) cc_final: 0.9235 (tpp)
REVERT: A  845 HIS cc_start: 0.9006 (t70) cc_final: 0.8764 (t70)
REVERT: A  900 MET cc_start: 0.9432 (ttp) cc_final: 0.9207 (tpt)
REVERT: A 1087 PHE cc_start: 0.9083 (m-10) cc_final: 0.8761 (p90)
REVERT: A 1261 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7657 (tm-30)
REVERT: A 1408 MET cc_start: 0.9507 (mmm) cc_final: 0.9254 (mtt)
REVERT: A 1416 MET cc_start: 0.9634 (mmt) cc_final: 0.9407 (mmp)
REVERT: A 1742 CYS cc_start: 0.6261 (OUTLIER) cc_final: 0.5279 (p)
REVERT: A 1781 MET cc_start: 0.8569 (mmt) cc_final: 0.8322 (mmp)
  outliers start: 83
  outliers final: 26
  residues processed: 193
  average time/residue: 0.1205
  time to fit residues: 31.3149
Evaluate side-chains
  115 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 85
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:   30.0000
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    9.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 424 GLN
A 532 HIS
A 661 HIS
A 713 GLN
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1317 HIS
A1411 GLN
A1428 GLN
A1523 ASN
A1582 HIS
** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1758 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.061534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.048646 restraints weight = 151239.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.049777 restraints weight = 105461.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.050552 restraints weight = 81261.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.051109 restraints weight = 67111.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.051531 restraints weight = 58225.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  11091  Z= 0.168
  Angle     :  0.749  10.586  15358  Z= 0.388
  Chirality :  0.043   0.258   1831
  Planarity :  0.006   0.072   1638
  Dihedral  : 20.824 179.381   2500
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 24.40
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.29 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  6.92 %
    Favored  : 92.57 %
  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 are not related in a simple way.
  whole: -2.49 (0.23), residues: 1111
  helix: -0.78 (0.20), residues: 576
  sheet: -2.65 (0.44), residues: 104
  loop : -2.50 (0.27), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 666 
 TYR   0.037   0.002   TYR A 757 
 PHE   0.021   0.002   PHE A1225 
 TRP   0.042   0.003   TRP A 341 
 HIS   0.005   0.001   HIS A 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (11091)
  covalent geometry    : angle       0.74907 (15358)
  hydrogen bonds       : bond        0.06790 (  521)
  hydrogen bonds       : angle       6.22576 ( 1438)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 0.339 
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: symmetry clash
   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: A  346 GLU cc_start: 0.9395 (tm-30) cc_final: 0.9104 (mp0)
REVERT: A  393 MET cc_start: 0.9169 (tpt) cc_final: 0.8409 (tpp)
REVERT: A  411 MET cc_start: 0.6946 (mtt) cc_final: 0.6571 (mtt)
REVERT: A  670 PHE cc_start: 0.9204 (m-80) cc_final: 0.8967 (m-80)
REVERT: A  746 MET cc_start: 0.9453 (tpt) cc_final: 0.8618 (mmm)
REVERT: A  763 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8390 (ttp-110)
REVERT: A  774 MET cc_start: 0.8657 (ttt) cc_final: 0.6534 (tpp)
REVERT: A 1234 MET cc_start: 0.8859 (tpt) cc_final: 0.8655 (tpt)
REVERT: A 1340 MET cc_start: 0.9035 (mmm) cc_final: 0.8581 (mmm)
REVERT: A 1570 PHE cc_start: 0.5069 (t80) cc_final: 0.4606 (t80)
REVERT: A 1576 LEU cc_start: 0.9578 (tt) cc_final: 0.9363 (tt)
REVERT: A 1646 LEU cc_start: 0.9161 (mm) cc_final: 0.8613 (mm)
  outliers start: 5
  outliers final: 1
  residues processed: 114
  average time/residue: 0.0985
  time to fit residues: 16.3914
Evaluate side-chains
  84 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0970
   chunk 9 optimal weight:    8.9990
   chunk 74 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   chunk 101 optimal weight:   30.0000
   chunk 95 optimal weight:   50.0000
   chunk 96 optimal weight:   30.0000
   chunk 39 optimal weight:   20.0000
   chunk 3 optimal weight:    6.9990
   overall best weight:    4.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 538 ASN
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1268 ASN
** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1758 ASN
A1776 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.060445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.047517 restraints weight = 152584.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.048598 restraints weight = 107600.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.049364 restraints weight = 83210.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.049898 restraints weight = 68562.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.050292 restraints weight = 59710.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  11091  Z= 0.168
  Angle     :  0.707  10.592  15358  Z= 0.365
  Chirality :  0.041   0.195   1831
  Planarity :  0.005   0.056   1638
  Dihedral  : 20.560 176.741   2500
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 24.40
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.10 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  6.00 %
    Favored  : 93.90 %
  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 are not related in a simple way.
  whole: -2.18 (0.24), residues: 1111
  helix: -0.46 (0.21), residues: 579
  sheet: -2.37 (0.50), residues: 87
  loop : -2.55 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1391 
 TYR   0.030   0.002   TYR A 757 
 PHE   0.026   0.002   PHE A 889 
 TRP   0.024   0.002   TRP A 341 
 HIS   0.006   0.001   HIS A 381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (11091)
  covalent geometry    : angle       0.70711 (15358)
  hydrogen bonds       : bond        0.06614 (  521)
  hydrogen bonds       : angle       5.91651 ( 1438)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.332 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  393 MET cc_start: 0.9187 (tpt) cc_final: 0.8530 (tpp)
REVERT: A  746 MET cc_start: 0.9468 (tpt) cc_final: 0.8483 (mmm)
REVERT: A  774 MET cc_start: 0.8610 (ttt) cc_final: 0.6859 (tpp)
REVERT: A 1340 MET cc_start: 0.9139 (mmm) cc_final: 0.8690 (mmm)
REVERT: A 1412 MET cc_start: 0.9424 (mmp) cc_final: 0.9114 (mmm)
REVERT: A 1570 PHE cc_start: 0.5345 (t80) cc_final: 0.5128 (t80)
REVERT: A 1576 LEU cc_start: 0.9570 (tt) cc_final: 0.9344 (tt)
REVERT: A 1724 MET cc_start: 0.7754 (mpp) cc_final: 0.7551 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0970
  time to fit residues: 14.4992
Evaluate side-chains
  78 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 88 optimal weight:    8.9990
   chunk 118 optimal weight:   20.0000
   chunk 91 optimal weight:    2.9990
   chunk 4 optimal weight:    9.9990
   chunk 5 optimal weight:    0.3980
   chunk 9 optimal weight:    8.9990
   chunk 70 optimal weight:    1.9990
   chunk 30 optimal weight:   30.0000
   chunk 97 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 GLN
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1268 ASN
** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1428 GLN
A1647 HIS
A1722 GLN
A1758 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.063059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.049977 restraints weight = 149618.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.051116 restraints weight = 104204.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.051901 restraints weight = 80189.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.052448 restraints weight = 66046.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 63)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.052886 restraints weight = 57255.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.3850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11091  Z= 0.132
  Angle     :  0.661  11.505  15358  Z= 0.334
  Chirality :  0.040   0.178   1831
  Planarity :  0.004   0.046   1638
  Dihedral  : 20.130 174.718   2500
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 19.16
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.74 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  4.48 %
    Favored  : 95.32 %
  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 are not related in a simple way.
  whole: -1.85 (0.24), residues: 1111
  helix: -0.09 (0.21), residues: 580
  sheet: -2.04 (0.52), residues: 87
  loop : -2.60 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1391 
 TYR   0.024   0.001   TYR A 757 
 PHE   0.020   0.001   PHE A 556 
 TRP   0.016   0.001   TRP A 341 
 HIS   0.004   0.001   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (11091)
  covalent geometry    : angle       0.66116 (15358)
  hydrogen bonds       : bond        0.06322 (  521)
  hydrogen bonds       : angle       5.57826 ( 1438)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.280 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  393 MET cc_start: 0.9181 (tpt) cc_final: 0.8544 (tpp)
REVERT: A  746 MET cc_start: 0.9567 (tpt) cc_final: 0.9120 (tpp)
REVERT: A 1234 MET cc_start: 0.8837 (tpt) cc_final: 0.8510 (tpp)
REVERT: A 1340 MET cc_start: 0.9025 (mmm) cc_final: 0.8508 (mmm)
REVERT: A 1412 MET cc_start: 0.9451 (mmp) cc_final: 0.9145 (mmm)
REVERT: A 1570 PHE cc_start: 0.5582 (t80) cc_final: 0.5317 (t80)
REVERT: A 1576 LEU cc_start: 0.9579 (tt) cc_final: 0.9376 (tt)
REVERT: A 1758 ASN cc_start: 0.5239 (OUTLIER) cc_final: 0.4764 (m-40)
  outliers start: 2
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0942
  time to fit residues: 15.0365
Evaluate side-chains
  81 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 55 optimal weight:   20.0000
   chunk 103 optimal weight:   30.0000
   chunk 67 optimal weight:   20.0000
   chunk 116 optimal weight:   20.0000
   chunk 56 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 46 optimal weight:   20.0000
   chunk 78 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 65 optimal weight:   20.0000
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1268 ASN
** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1420 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.060893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.047837 restraints weight = 150417.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.048930 restraints weight = 106344.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.049710 restraints weight = 82898.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.050250 restraints weight = 68739.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.050683 restraints weight = 59808.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.4119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11091  Z= 0.153
  Angle     :  0.679   9.251  15358  Z= 0.347
  Chirality :  0.040   0.197   1831
  Planarity :  0.005   0.055   1638
  Dihedral  : 20.147 173.025   2500
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 24.21
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.73 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  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 are not related in a simple way.
  whole: -1.86 (0.24), residues: 1111
  helix: -0.16 (0.21), residues: 587
  sheet: -1.94 (0.53), residues: 82
  loop : -2.56 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1391 
 TYR   0.020   0.001   TYR A 757 
 PHE   0.019   0.002   PHE A1225 
 TRP   0.013   0.002   TRP A 341 
 HIS   0.005   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (11091)
  covalent geometry    : angle       0.67872 (15358)
  hydrogen bonds       : bond        0.06579 (  521)
  hydrogen bonds       : angle       5.62745 ( 1438)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.233 
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: symmetry clash
   revert: symmetry clash
REVERT: A  393 MET cc_start: 0.9126 (tpt) cc_final: 0.8527 (tpp)
REVERT: A  411 MET cc_start: 0.6237 (mtt) cc_final: 0.5740 (mtt)
REVERT: A  746 MET cc_start: 0.9577 (tpt) cc_final: 0.9115 (tpp)
REVERT: A 1037 LYS cc_start: 0.8828 (pttm) cc_final: 0.7847 (mptt)
REVERT: A 1234 MET cc_start: 0.8861 (tpt) cc_final: 0.8653 (tpt)
REVERT: A 1340 MET cc_start: 0.8984 (mmm) cc_final: 0.8516 (mmm)
REVERT: A 1412 MET cc_start: 0.9467 (mmp) cc_final: 0.9164 (mmm)
REVERT: A 1570 PHE cc_start: 0.6000 (t80) cc_final: 0.5375 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0889
  time to fit residues: 13.1811
Evaluate side-chains
  75 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 62 optimal weight:   30.0000
   chunk 20 optimal weight:   20.0000
   chunk 69 optimal weight:    7.9990
   chunk 82 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 12 optimal weight:   20.0000
   chunk 50 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0030
   chunk 66 optimal weight:    9.9990
   overall best weight:    3.9998

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 741 GLN
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1268 ASN
** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1633 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 = 0.3545 r_free = 0.3545 target = 0.061101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.047978 restraints weight = 149840.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.049037 restraints weight = 106985.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.049784 restraints weight = 83501.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.050335 restraints weight = 69367.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.050746 restraints weight = 60345.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.4483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11091  Z= 0.152
  Angle     :  0.680  13.425  15358  Z= 0.345
  Chirality :  0.040   0.184   1831
  Planarity :  0.005   0.046   1638
  Dihedral  : 20.042 171.371   2500
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 23.97
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.46 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  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 are not related in a simple way.
  whole: -1.79 (0.24), residues: 1111
  helix: -0.08 (0.21), residues: 591
  sheet: -1.94 (0.51), residues: 86
  loop : -2.58 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1391 
 TYR   0.020   0.002   TYR A 757 
 PHE   0.015   0.002   PHE A 889 
 TRP   0.012   0.002   TRP A1104 
 HIS   0.006   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (11091)
  covalent geometry    : angle       0.68009 (15358)
  hydrogen bonds       : bond        0.06625 (  521)
  hydrogen bonds       : angle       5.60744 ( 1438)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.338 
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: symmetry clash
   revert: symmetry clash
REVERT: A  393 MET cc_start: 0.9243 (tpt) cc_final: 0.8675 (tpp)
REVERT: A  411 MET cc_start: 0.6263 (mtt) cc_final: 0.5854 (mtm)
REVERT: A  746 MET cc_start: 0.9526 (tpt) cc_final: 0.9035 (tpp)
REVERT: A 1037 LYS cc_start: 0.8964 (pttm) cc_final: 0.7790 (mppt)
REVERT: A 1234 MET cc_start: 0.8964 (tpt) cc_final: 0.8737 (tpt)
REVERT: A 1340 MET cc_start: 0.8915 (mmm) cc_final: 0.8458 (mmm)
REVERT: A 1367 SER cc_start: 0.8610 (m) cc_final: 0.8372 (p)
REVERT: A 1412 MET cc_start: 0.9429 (mmp) cc_final: 0.9131 (mmm)
REVERT: A 1570 PHE cc_start: 0.5922 (t80) cc_final: 0.5588 (t80)
REVERT: A 1576 LEU cc_start: 0.9610 (tt) cc_final: 0.9409 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0938
  time to fit residues: 13.9076
Evaluate side-chains
  77 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 104 optimal weight:   20.0000
   chunk 44 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 90 optimal weight:   20.0000
   chunk 15 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 70 optimal weight:   20.0000
   chunk 9 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 788 ASN
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1261 GLN
A1268 ASN
** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.060319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.047075 restraints weight = 149538.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.048165 restraints weight = 107206.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.048912 restraints weight = 83666.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.049475 restraints weight = 69582.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.049883 restraints weight = 60489.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.4769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11091  Z= 0.163
  Angle     :  0.707  13.430  15358  Z= 0.358
  Chirality :  0.041   0.182   1831
  Planarity :  0.005   0.047   1638
  Dihedral  : 20.018 169.083   2500
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 25.85
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.09 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  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 are not related in a simple way.
  whole: -1.75 (0.24), residues: 1111
  helix: -0.06 (0.21), residues: 589
  sheet: -1.92 (0.53), residues: 82
  loop : -2.55 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1391 
 TYR   0.017   0.002   TYR A 757 
 PHE   0.016   0.002   PHE A 889 
 TRP   0.019   0.002   TRP A1104 
 HIS   0.004   0.001   HIS A1524 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (11091)
  covalent geometry    : angle       0.70705 (15358)
  hydrogen bonds       : bond        0.06850 (  521)
  hydrogen bonds       : angle       5.66075 ( 1438)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  393 MET cc_start: 0.9262 (tpt) cc_final: 0.8685 (tpp)
REVERT: A  411 MET cc_start: 0.6639 (mtt) cc_final: 0.6211 (mtm)
REVERT: A  746 MET cc_start: 0.9443 (tpt) cc_final: 0.8966 (tpt)
REVERT: A 1037 LYS cc_start: 0.8868 (pttm) cc_final: 0.7525 (mppt)
REVERT: A 1234 MET cc_start: 0.9017 (tpt) cc_final: 0.8775 (tpt)
REVERT: A 1340 MET cc_start: 0.8837 (mmm) cc_final: 0.8381 (mmm)
REVERT: A 1367 SER cc_start: 0.8702 (m) cc_final: 0.8414 (p)
REVERT: A 1412 MET cc_start: 0.9419 (mmp) cc_final: 0.9099 (mmm)
REVERT: A 1570 PHE cc_start: 0.5860 (t80) cc_final: 0.5496 (t80)
REVERT: A 1576 LEU cc_start: 0.9591 (tt) cc_final: 0.9344 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0830
  time to fit residues: 11.9507
Evaluate side-chains
  74 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 24 optimal weight:   20.0000
   chunk 84 optimal weight:    0.0470
   chunk 30 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 106 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 75 optimal weight:    8.9990
   chunk 90 optimal weight:    7.9990
   overall best weight:    3.1884

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

Flipped N/Q/H residues before XYZ refinement:
** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 GLN
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1268 ASN
** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1523 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.062031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.048851 restraints weight = 147709.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.049988 restraints weight = 104504.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.050758 restraints weight = 81046.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.051284 restraints weight = 66996.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.051733 restraints weight = 58295.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.5055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11091  Z= 0.141
  Angle     :  0.682  13.306  15358  Z= 0.345
  Chirality :  0.040   0.179   1831
  Planarity :  0.004   0.047   1638
  Dihedral  : 19.785 167.023   2500
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 22.96
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.55 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  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 are not related in a simple way.
  whole: -1.69 (0.24), residues: 1111
  helix: -0.01 (0.21), residues: 592
  sheet: -1.77 (0.55), residues: 82
  loop : -2.55 (0.27), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1564 
 TYR   0.028   0.001   TYR A 757 
 PHE   0.017   0.001   PHE A 268 
 TRP   0.013   0.002   TRP A1104 
 HIS   0.004   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (11091)
  covalent geometry    : angle       0.68206 (15358)
  hydrogen bonds       : bond        0.06769 (  521)
  hydrogen bonds       : angle       5.52431 ( 1438)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.234 
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: A  393 MET cc_start: 0.9317 (tpt) cc_final: 0.8826 (tpp)
REVERT: A  411 MET cc_start: 0.6267 (mtt) cc_final: 0.5923 (mtm)
REVERT: A  670 PHE cc_start: 0.9369 (m-80) cc_final: 0.8993 (m-10)
REVERT: A  746 MET cc_start: 0.9432 (tpt) cc_final: 0.8895 (tpt)
REVERT: A  843 LEU cc_start: 0.9250 (mm) cc_final: 0.9018 (tp)
REVERT: A  900 MET cc_start: 0.9601 (mmp) cc_final: 0.9369 (mmm)
REVERT: A 1037 LYS cc_start: 0.8840 (pttm) cc_final: 0.7461 (mppt)
REVERT: A 1234 MET cc_start: 0.9015 (tpt) cc_final: 0.8767 (tpt)
REVERT: A 1340 MET cc_start: 0.8813 (mmm) cc_final: 0.8357 (mmm)
REVERT: A 1367 SER cc_start: 0.8773 (m) cc_final: 0.8473 (p)
REVERT: A 1412 MET cc_start: 0.9447 (mmp) cc_final: 0.9125 (mmm)
REVERT: A 1597 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8576 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0808
  time to fit residues: 12.7622
Evaluate side-chains
  75 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   chunk 72 optimal weight:   20.0000
   chunk 5 optimal weight:    0.0070
   chunk 119 optimal weight:   30.0000
   chunk 63 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 107 optimal weight:   20.0000
   chunk 104 optimal weight:   30.0000
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    3.0006

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

Flipped N/Q/H residues before XYZ refinement:
** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 538 ASN
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1261 GLN
A1268 ASN
** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.061891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.048728 restraints weight = 148743.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.049816 restraints weight = 105072.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.050591 restraints weight = 81701.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.051149 restraints weight = 67637.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.051533 restraints weight = 58703.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.5288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11091  Z= 0.138
  Angle     :  0.676  13.033  15358  Z= 0.342
  Chirality :  0.040   0.241   1831
  Planarity :  0.004   0.042   1638
  Dihedral  : 19.630 164.652   2500
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 21.85
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.82 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  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 are not related in a simple way.
  whole: -1.64 (0.24), residues: 1111
  helix:  0.04 (0.21), residues: 593
  sheet: -1.78 (0.54), residues: 83
  loop : -2.53 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1564 
 TYR   0.027   0.002   TYR A 757 
 PHE   0.023   0.002   PHE A1570 
 TRP   0.012   0.001   TRP A1104 
 HIS   0.005   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11091)
  covalent geometry    : angle       0.67646 (15358)
  hydrogen bonds       : bond        0.06797 (  521)
  hydrogen bonds       : angle       5.43582 ( 1438)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.331 
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: symmetry clash
REVERT: A  393 MET cc_start: 0.9314 (tpt) cc_final: 0.8859 (tpp)
REVERT: A  411 MET cc_start: 0.6330 (mtt) cc_final: 0.5938 (mtm)
REVERT: A  670 PHE cc_start: 0.9357 (m-80) cc_final: 0.9062 (m-10)
REVERT: A  746 MET cc_start: 0.9420 (tpt) cc_final: 0.8960 (tpt)
REVERT: A  774 MET cc_start: 0.8309 (ttt) cc_final: 0.7046 (tpp)
REVERT: A  843 LEU cc_start: 0.9240 (mm) cc_final: 0.9024 (tp)
REVERT: A  900 MET cc_start: 0.9571 (mmp) cc_final: 0.9314 (mmm)
REVERT: A 1037 LYS cc_start: 0.8949 (pttm) cc_final: 0.7954 (mptt)
REVERT: A 1234 MET cc_start: 0.9010 (tpt) cc_final: 0.8757 (tpt)
REVERT: A 1340 MET cc_start: 0.8826 (mmm) cc_final: 0.8378 (mmm)
REVERT: A 1367 SER cc_start: 0.8691 (m) cc_final: 0.8374 (p)
REVERT: A 1412 MET cc_start: 0.9419 (mmp) cc_final: 0.9105 (mmm)
REVERT: A 1724 MET cc_start: 0.8011 (mpp) cc_final: 0.7561 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0892
  time to fit residues: 13.4080
Evaluate side-chains
  75 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 79 optimal weight:    7.9990
   chunk 113 optimal weight:   30.0000
   chunk 119 optimal weight:   30.0000
   chunk 6 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9980
   chunk 111 optimal weight:    0.0050
   chunk 94 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    2.1398

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

Flipped N/Q/H residues before XYZ refinement:
** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1268 ASN
** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1404 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 = 0.3588 r_free = 0.3588 target = 0.062971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.049791 restraints weight = 146126.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.050927 restraints weight = 103990.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.051699 restraints weight = 80493.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.052298 restraints weight = 66629.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.052718 restraints weight = 57410.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.5566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11091  Z= 0.129
  Angle     :  0.671  12.548  15358  Z= 0.335
  Chirality :  0.039   0.182   1831
  Planarity :  0.004   0.042   1638
  Dihedral  : 19.396 162.217   2500
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 19.30
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.65 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    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 are not related in a simple way.
  whole: -1.46 (0.24), residues: 1111
  helix:  0.20 (0.21), residues: 590
  sheet: -1.45 (0.55), residues: 83
  loop : -2.52 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1564 
 TYR   0.027   0.001   TYR A 757 
 PHE   0.016   0.001   PHE A 889 
 TRP   0.012   0.001   TRP A 341 
 HIS   0.005   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (11091)
  covalent geometry    : angle       0.67148 (15358)
  hydrogen bonds       : bond        0.06823 (  521)
  hydrogen bonds       : angle       5.33837 ( 1438)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.383 
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: symmetry clash
REVERT: A  393 MET cc_start: 0.9298 (tpt) cc_final: 0.8852 (tpp)
REVERT: A  411 MET cc_start: 0.6203 (mtt) cc_final: 0.5896 (mtm)
REVERT: A  670 PHE cc_start: 0.9315 (m-80) cc_final: 0.9070 (m-10)
REVERT: A  746 MET cc_start: 0.9452 (tpt) cc_final: 0.8982 (tpt)
REVERT: A  774 MET cc_start: 0.8270 (ttt) cc_final: 0.6927 (tpp)
REVERT: A 1037 LYS cc_start: 0.9072 (pttm) cc_final: 0.7872 (mptt)
REVERT: A 1234 MET cc_start: 0.9029 (tpt) cc_final: 0.8790 (tpt)
REVERT: A 1340 MET cc_start: 0.8768 (mmm) cc_final: 0.8328 (mmm)
REVERT: A 1367 SER cc_start: 0.8667 (m) cc_final: 0.8338 (p)
REVERT: A 1412 MET cc_start: 0.9426 (mmp) cc_final: 0.9113 (mmm)
REVERT: A 1724 MET cc_start: 0.8048 (mpp) cc_final: 0.7645 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0850
  time to fit residues: 12.9728
Evaluate side-chains
  77 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 44 optimal weight:    0.0010
   chunk 83 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   chunk 52 optimal weight:   30.0000
   chunk 97 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   chunk 102 optimal weight:    5.9990
   chunk 112 optimal weight:    7.9990
   chunk 100 optimal weight:   10.0000
   overall best weight:    1.9592

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1268 ASN
** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1404 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 = 0.3600 r_free = 0.3600 target = 0.063594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.050442 restraints weight = 147095.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.051470 restraints weight = 102516.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.052235 restraints weight = 79929.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.052780 restraints weight = 66279.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.053229 restraints weight = 57556.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.5812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11091  Z= 0.126
  Angle     :  0.662  12.025  15358  Z= 0.330
  Chirality :  0.039   0.184   1831
  Planarity :  0.004   0.044   1638
  Dihedral  : 19.219 161.957   2500
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 18.00
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.92 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  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 are not related in a simple way.
  whole: -1.34 (0.24), residues: 1111
  helix:  0.29 (0.21), residues: 591
  sheet: -1.41 (0.55), residues: 83
  loop : -2.46 (0.26), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1564 
 TYR   0.026   0.001   TYR A 757 
 PHE   0.018   0.001   PHE A 889 
 TRP   0.013   0.001   TRP A 341 
 HIS   0.004   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (11091)
  covalent geometry    : angle       0.66211 (15358)
  hydrogen bonds       : bond        0.06840 (  521)
  hydrogen bonds       : angle       5.28790 ( 1438)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1798.41 seconds
wall clock time: 31 minutes 59.30 seconds (1919.30 seconds total)