Starting phenix.real_space_refine
on Wed Mar  4 06:12:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7eld_31181/03_2026/7eld_31181.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eld_31181/03_2026/7eld_31181.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eld_31181/03_2026/7eld_31181.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eld_31181/03_2026/7eld_31181.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7eld_31181/03_2026/7eld_31181.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eld_31181/03_2026/7eld_31181.map"
  }
  resolution = 4.6
  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     109      5.49       5
     S      60      5.16       5
     C    6758      2.51       5
     N    1946      2.21       5
     O    2409      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11282
  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: "B"
      Number of atoms: 2306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 2306
          Classifications: {'RNA': 109}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 48, 'rna3p_pyr': 56}
          Link IDs: {'rna2p': 4, 'rna3p': 104}
          Chain breaks: 6
  Time building chain proxies: 2.33, per 1000 atoms: 0.21
  Number of scatterers: 11282
  At special positions: 0
  Unit cell: (95.316, 110.526, 188.604, 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     109     15.00
     O    2409      8.00
     N    1946      7.00
     C    6758      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: 0.85
  Conformation dependent library (CDL) restraints added in 443.9 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:
      46 helices and 8 sheets defined
      57.7% alpha, 4.7% beta
      43 base pairs and 83 stacking pairs defined.
    Time for finding SS restraints: 1.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 250 through 263
    Processing helix  chain 'A' and resid 274 through 289
      removed outlier: 3.523A  pdb=" N   ASP A 289 " --> pdb=" O   SER A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 297
      removed outlier: 4.099A  pdb=" N   MET A 297 " --> pdb=" O   ASN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 319
      removed outlier: 3.847A  pdb=" N   ASN A 318 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLN A 319 " --> pdb=" O   VAL A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 348
    Processing helix  chain 'A' and resid 354 through 363
    Processing helix  chain 'A' and resid 368 through 372
      removed outlier: 3.980A  pdb=" N   ILE A 372 " --> pdb=" O   MET A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 398
      removed outlier: 3.655A  pdb=" N   LEU A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE A 396 " --> pdb=" O   VAL A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 439
    Processing helix  chain 'A' and resid 472 through 493
      removed outlier: 3.685A  pdb=" N   THR A 477 " --> pdb=" O   SER A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 567
      removed outlier: 6.980A  pdb=" N   GLN A 546 " --> pdb=" O   ALA A 542 " (cutoff:3.500A)
      removed outlier: 9.432A  pdb=" N   TRP A 547 " --> pdb=" O   GLU A 543 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   CYS A 548 " --> pdb=" O   LEU A 544 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LYS A 551 " --> pdb=" O   TRP A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 594
      removed outlier: 4.276A  pdb=" N   GLU A 589 " --> pdb=" O   LEU A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 661
      removed outlier: 3.856A  pdb=" N   HIS A 661 " --> pdb=" O   LEU A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 664
      No H-bonds generated for 'chain 'A' and resid 662 through 664'
    Processing helix  chain 'A' and resid 673 through 687
      Proline residue:  A 681  - end of helix
      removed outlier: 3.650A  pdb=" N   LEU A 687 " --> pdb=" O   VAL A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 721
      removed outlier: 3.592A  pdb=" N   ASP A 721 " --> pdb=" O   SER A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 728
    Processing helix  chain 'A' and resid 753 through 764
    Processing helix  chain 'A' and resid 781 through 800
      removed outlier: 3.905A  pdb=" N   PHE A 785 " --> pdb=" O   SER A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 809
    Processing helix  chain 'A' and resid 810 through 817
    Processing helix  chain 'A' and resid 827 through 851
      removed outlier: 4.079A  pdb=" N   THR A 831 " --> pdb=" O   LYS A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 920
    Processing helix  chain 'A' and resid 1049 through 1064
    Processing helix  chain 'A' and resid 1064 through 1069
    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: 3.580A  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
    Processing helix  chain 'A' and resid 1356 through 1364
    Processing helix  chain 'A' and resid 1374 through 1397
    Processing helix  chain 'A' and resid 1401 through 1414
    Processing helix  chain 'A' and resid 1414 through 1426
    Processing helix  chain 'A' and resid 1501 through 1517
    Processing helix  chain 'A' and resid 1518 through 1529
    Processing helix  chain 'A' and resid 1559 through 1567
    Processing helix  chain 'A' and resid 1572 through 1581
      removed outlier: 3.707A  pdb=" N   LEU A1576 " --> pdb=" O   GLU A1572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1592 through 1615
      removed outlier: 4.443A  pdb=" N   LEU A1596 " --> pdb=" O   CYS A1592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1620 through 1632
    Processing helix  chain 'A' and resid 1633 through 1644
    Processing helix  chain 'A' and resid 1645 through 1650
    Processing helix  chain 'A' and resid 1654 through 1668
    Processing helix  chain 'A' and resid 1690 through 1706
    Processing helix  chain 'A' and resid 1709 through 1726
      removed outlier: 3.524A  pdb=" N   ALA A1713 " --> pdb=" O   ASP A1709 " (cutoff:3.500A)
      Proline residue:  A1719  - end of helix
      Proline residue:  A1723  - end of helix
      removed outlier: 3.913A  pdb=" N   THR A1726 " --> pdb=" O   GLN A1722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1733 through 1742
    Processing helix  chain 'A' and resid 1780 through 1794
    Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 266
    Processing sheet with id=AA2, first strand: chain 'A' and resid 324 through 326
      removed outlier: 6.623A  pdb=" N   GLY A 325 " --> pdb=" O   VAL A 352 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE A 301 " --> pdb=" O   MET A 353 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   VAL A 300 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 460 through 464
      removed outlier: 5.453A  pdb=" N   ILE A 461 " --> pdb=" O   LEU A 773 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   VAL A 775 " --> pdb=" O   ILE A 461 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   VAL A 463 " --> pdb=" O   VAL A 775 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 862 through 867
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1036 through 1041
      removed outlier: 4.343A  pdb=" N   PHE A1009 " --> pdb=" O   LYS A 981 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU A1086 " --> pdb=" O   LEU A1012 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1211 through 1212
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1230 through 1231
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1760 through 1761
      removed outlier: 3.683A  pdb=" N   ALA A1760 " --> pdb=" O   GLY A1772 " (cutoff:3.500A)

    467 hydrogen bonds defined for protein.
    1380 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      103 hydrogen bonds
      194 hydrogen bond angles
      0 basepair planarities
      43 basepair parallelities
      83 stacking parallelities
  Total time for adding SS restraints: 3.08

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1883
        1.32 -     1.45: 3390
        1.45 -     1.57: 6121
        1.57 -     1.69: 211
        1.69 -     1.81: 96
  Bond restraints: 11701
  Sorted by residual:
  bond pdb=" C   VAL A 828 "
       pdb=" O   VAL A 828 "
    ideal  model  delta    sigma   weight residual
    1.237  1.321 -0.084 1.19e-02 7.06e+03 4.97e+01
  bond pdb=" C   VAL A 841 "
       pdb=" O   VAL A 841 "
    ideal  model  delta    sigma   weight residual
    1.237  1.306 -0.069 1.13e-02 7.83e+03 3.74e+01
  bond pdb=" C   ASN A 838 "
       pdb=" O   ASN A 838 "
    ideal  model  delta    sigma   weight residual
    1.237  1.301 -0.064 1.17e-02 7.31e+03 3.03e+01
  bond pdb=" C   TYR A 847 "
       pdb=" O   TYR A 847 "
    ideal  model  delta    sigma   weight residual
    1.237  1.298 -0.062 1.17e-02 7.31e+03 2.77e+01
  bond pdb=" N   VAL A 303 "
       pdb=" CA  VAL A 303 "
    ideal  model  delta    sigma   weight residual
    1.454  1.494 -0.040 7.70e-03 1.69e+04 2.69e+01
  ... (remaining 11696 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 13871
        2.21 -     4.43: 2358
        4.43 -     6.64: 60
        6.64 -     8.85: 9
        8.85 -    11.07: 2
  Bond angle restraints: 16300
  Sorted by residual:
  angle pdb=" O3'   U B 115 "
        pdb=" C3'   U B 115 "
        pdb=" C2'   U B 115 "
      ideal   model   delta    sigma   weight residual
     109.50  120.57  -11.07 1.50e+00 4.44e-01 5.44e+01
  angle pdb=" CA  LYS A 827 "
        pdb=" C   LYS A 827 "
        pdb=" N   VAL A 828 "
      ideal   model   delta    sigma   weight residual
     115.27  123.61   -8.34 1.34e+00 5.57e-01 3.87e+01
  angle pdb=" O   LYS A 827 "
        pdb=" C   LYS A 827 "
        pdb=" N   VAL A 828 "
      ideal   model   delta    sigma   weight residual
     122.79  116.30    6.49 1.14e+00 7.69e-01 3.24e+01
  angle pdb=" C   ALA A 840 "
        pdb=" N   VAL A 841 "
        pdb=" CA  VAL A 841 "
      ideal   model   delta    sigma   weight residual
     120.56  113.45    7.11 1.26e+00 6.30e-01 3.19e+01
  angle pdb=" C   HIS A 874 "
        pdb=" N   THR A 875 "
        pdb=" CA  THR A 875 "
      ideal   model   delta    sigma   weight residual
     121.54  131.82  -10.28 1.91e+00 2.74e-01 2.90e+01
  ... (remaining 16295 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.28: 6723
       35.28 -    70.55: 466
       70.55 -   105.83: 47
      105.83 -   141.10: 2
      141.10 -   176.38: 1
  Dihedral angle restraints: 7239
    sinusoidal: 3913
      harmonic: 3326
  Sorted by residual:
  dihedral pdb=" C5'   U B 115 "
           pdb=" C4'   U B 115 "
           pdb=" C3'   U B 115 "
           pdb=" O3'   U B 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   89.74   57.26     1      8.00e+00 1.56e-02 6.89e+01
  dihedral pdb=" C   LEU A 851 "
           pdb=" N   LEU A 851 "
           pdb=" CA  LEU A 851 "
           pdb=" CB  LEU A 851 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.27   15.67     0      2.50e+00 1.60e-01 3.93e+01
  dihedral pdb=" O4'   C B  27 "
           pdb=" C1'   C B  27 "
           pdb=" N1    C B  27 "
           pdb=" C2    C B  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -77.36  -82.64     1      1.50e+01 4.44e-03 3.72e+01
  ... (remaining 7236 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 1370
       0.122 -    0.245: 576
       0.245 -    0.367: 11
       0.367 -    0.489: 2
       0.489 -    0.611: 2
  Chirality restraints: 1961
  Sorted by residual:
  chirality pdb=" C3'   U B 115 "
            pdb=" C4'   U B 115 "
            pdb=" O3'   U B 115 "
            pdb=" C2'   U B 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.13   -0.61 2.00e-01 2.50e+01 9.34e+00
  chirality pdb=" CA  LEU A 851 "
            pdb=" N   LEU A 851 "
            pdb=" C   LEU A 851 "
            pdb=" CB  LEU A 851 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.35e+00
  chirality pdb=" CA  ASN A1636 "
            pdb=" N   ASN A1636 "
            pdb=" C   ASN A1636 "
            pdb=" CB  ASN A1636 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.54e+00
  ... (remaining 1958 not shown)

  Planarity restraints: 1664
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 827 "    0.025 2.00e-02 2.50e+03   4.78e-02 2.29e+01
        pdb=" C   LYS A 827 "   -0.083 2.00e-02 2.50e+03
        pdb=" O   LYS A 827 "    0.029 2.00e-02 2.50e+03
        pdb=" N   VAL A 828 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 848 "   -0.017 2.00e-02 2.50e+03   3.53e-02 1.25e+01
        pdb=" C   CYS A 848 "    0.061 2.00e-02 2.50e+03
        pdb=" O   CYS A 848 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   SER A 849 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 841 "   -0.018 2.00e-02 2.50e+03   3.52e-02 1.24e+01
        pdb=" C   VAL A 841 "    0.061 2.00e-02 2.50e+03
        pdb=" O   VAL A 841 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLY A 842 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1661 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 4515
        2.94 -     3.43: 11264
        3.43 -     3.92: 21762
        3.92 -     4.41: 24346
        4.41 -     4.90: 33229
  Nonbonded interactions: 95116
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 874 "
            pdb=" O   THR A 875 "
     model   vdw
     2.446 3.040
  nonbonded pdb=" O5'   G B -13 "
            pdb=" O4'   G B -13 "
     model   vdw
     2.484 2.432
  nonbonded pdb=" O   GLU A 799 "
            pdb=" N   ILE A 801 "
     model   vdw
     2.495 3.120
  nonbonded pdb=" O5'   A B -10 "
            pdb=" O4'   A B -10 "
     model   vdw
     2.498 2.432
  nonbonded pdb=" O5'   C B  79 "
            pdb=" O4'   C B  79 "
     model   vdw
     2.508 2.432
  ... (remaining 95111 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:             0.480
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.530
  Find NCS groups from input model:        0.040
  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:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4880
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      :  0.012   0.084  11701  Z= 0.900
  Angle     :  1.409  11.065  16300  Z= 1.103
  Chirality :  0.108   0.611   1961
  Planarity :  0.005   0.059   1664
  Dihedral  : 20.425 176.377   5079
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  :  2.88 %
    Favored  : 96.22 %
  Rotamer:
    Outliers : 10.68 %
    Allowed  : 12.31 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.56 %
  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:  3.37 (0.24), residues: 1111
  helix:  4.32 (0.18), residues: 605
  sheet:  0.85 (0.57), residues: 83
  loop : -0.80 (0.25), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1062 
 TYR   0.011   0.002   TYR A 757 
 PHE   0.010   0.001   PHE A1613 
 TRP   0.009   0.001   TRP A 547 
 HIS   0.009   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.01159 (11701)
  covalent geometry    : angle       1.40940 (16300)
  hydrogen bonds       : bond        0.16830 (  570)
  hydrogen bonds       : angle       8.10693 ( 1574)

*********************** 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
  237 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 105
    poor density    : 132
  time to evaluate  : 0.400 
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: symmetry clash
REVERT: A  397 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7906 (p90)
REVERT: A  412 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8100 (t)
REVERT: A  434 LEU cc_start: 0.9705 (tp) cc_final: 0.9439 (mm)
REVERT: A  474 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9006 (pp)
REVERT: A  552 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8801 (m)
REVERT: A  556 PHE cc_start: 0.9188 (m-10) cc_final: 0.8982 (m-80)
REVERT: A  794 GLU cc_start: 0.9450 (OUTLIER) cc_final: 0.9125 (pt0)
REVERT: A  803 ARG cc_start: 0.9618 (mtp85) cc_final: 0.9362 (mmp-170)
REVERT: A  883 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7579 (mm)
REVERT: A  976 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8295 (p)
REVERT: A 1200 MET cc_start: 0.7283 (ttm) cc_final: 0.7065 (ttm)
REVERT: A 1371 THR cc_start: 0.7332 (OUTLIER) cc_final: 0.7104 (p)
REVERT: A 1416 MET cc_start: 0.8760 (mmt) cc_final: 0.8411 (mmm)
REVERT: A 1497 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8946 (pt)
  outliers start: 105
  outliers final: 25
  residues processed: 222
  average time/residue: 0.1094
  time to fit residues: 33.9894
Evaluate side-chains
  116 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 82
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:   30.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    9.9990
   chunk 117 optimal weight:   30.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
A 319 GLN
A 333 GLN
** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 791 ASN
A1328 GLN
A1420 GLN
A1739 GLN
A1776 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.046578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.035740 restraints weight = 172251.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.036372 restraints weight = 134602.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.036859 restraints weight = 112193.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.037200 restraints weight = 97440.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.037471 restraints weight = 87730.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11701  Z= 0.192
  Angle     :  0.722   9.203  16300  Z= 0.386
  Chirality :  0.042   0.244   1961
  Planarity :  0.005   0.067   1664
  Dihedral  : 21.638 172.722   2889
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 21.89
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  2.61 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  3.15 %
    Favored  : 96.44 %
  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:  1.39 (0.24), residues: 1111
  helix:  2.26 (0.19), residues: 623
  sheet: -0.37 (0.51), residues: 95
  loop : -0.98 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 317 
 TYR   0.029   0.002   TYR A1513 
 PHE   0.025   0.003   PHE A1372 
 TRP   0.023   0.003   TRP A1528 
 HIS   0.009   0.002   HIS A1401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (11701)
  covalent geometry    : angle       0.72166 (16300)
  hydrogen bonds       : bond        0.06526 (  570)
  hydrogen bonds       : angle       4.93845 ( 1574)

*********************** 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
  93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.325 
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  323 GLN cc_start: 0.9468 (mp10) cc_final: 0.9258 (mp10)
REVERT: A  865 MET cc_start: 0.7578 (pmm) cc_final: 0.6872 (tpp)
REVERT: A 1408 MET cc_start: 0.9769 (mtm) cc_final: 0.9459 (mtp)
REVERT: A 1416 MET cc_start: 0.8721 (mmt) cc_final: 0.8199 (mmm)
  outliers start: 4
  outliers final: 1
  residues processed: 93
  average time/residue: 0.1223
  time to fit residues: 15.8678
Evaluate side-chains
  67 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 75 optimal weight:   30.0000
   chunk 52 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 116 optimal weight:   20.0000
   chunk 56 optimal weight:    7.9990
   chunk 121 optimal weight:   40.0000
   chunk 23 optimal weight:    6.9990
   chunk 44 optimal weight:    8.9990
   chunk 10 optimal weight:   30.0000
   chunk 31 optimal weight:    0.6980
   overall best weight:    4.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 287 HIS
A 433 ASN
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1582 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.045152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.034518 restraints weight = 176162.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.035148 restraints weight = 137924.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.035606 restraints weight = 114852.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.035911 restraints weight = 100015.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.036071 restraints weight = 90786.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11701  Z= 0.147
  Angle     :  0.654   9.188  16300  Z= 0.345
  Chirality :  0.039   0.205   1961
  Planarity :  0.005   0.099   1664
  Dihedral  : 21.625 171.657   2889
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 19.81
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  3.33 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.07 %
    Favored  : 95.83 %
  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:  0.76 (0.24), residues: 1111
  helix:  1.69 (0.20), residues: 618
  sheet: -0.48 (0.55), residues: 86
  loop : -1.13 (0.28), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 763 
 TYR   0.015   0.001   TYR A 771 
 PHE   0.024   0.002   PHE A 785 
 TRP   0.019   0.002   TRP A 341 
 HIS   0.004   0.001   HIS A1401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (11701)
  covalent geometry    : angle       0.65429 (16300)
  hydrogen bonds       : bond        0.05696 (  570)
  hydrogen bonds       : angle       4.79154 ( 1574)

*********************** 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
  81 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.252 
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  369 MET cc_start: 0.4138 (mtp) cc_final: 0.3816 (mtp)
REVERT: A  474 LEU cc_start: 0.9367 (mm) cc_final: 0.9101 (pp)
REVERT: A  865 MET cc_start: 0.7628 (pmm) cc_final: 0.6666 (tpp)
REVERT: A 1026 MET cc_start: 0.8962 (mpp) cc_final: 0.8720 (mpp)
REVERT: A 1334 MET cc_start: 0.9402 (tpt) cc_final: 0.9202 (tpt)
REVERT: A 1408 MET cc_start: 0.9754 (mtm) cc_final: 0.9436 (mtp)
REVERT: A 1412 MET cc_start: 0.8191 (mtm) cc_final: 0.7930 (mtm)
REVERT: A 1416 MET cc_start: 0.8721 (mmt) cc_final: 0.8188 (mmm)
REVERT: A 1637 PHE cc_start: 0.9774 (m-80) cc_final: 0.9559 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0987
  time to fit residues: 11.6249
Evaluate side-chains
  63 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 36 optimal weight:   20.0000
   chunk 52 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 111 optimal weight:    8.9990
   chunk 96 optimal weight:    8.9990
   chunk 118 optimal weight:   40.0000
   chunk 20 optimal weight:    4.9990
   chunk 112 optimal weight:   10.0000
   chunk 104 optimal weight:    7.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 984 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.044288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.033754 restraints weight = 177068.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.034324 restraints weight = 140739.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.034720 restraints weight = 118847.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.035046 restraints weight = 104906.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.035269 restraints weight = 95199.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.5116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11701  Z= 0.140
  Angle     :  0.627   7.988  16300  Z= 0.328
  Chirality :  0.038   0.217   1961
  Planarity :  0.005   0.091   1664
  Dihedral  : 21.435 172.156   2889
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 19.81
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  3.87 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.26 %
    Favored  : 96.64 %
  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:  0.56 (0.24), residues: 1111
  helix:  1.62 (0.20), residues: 613
  sheet: -0.55 (0.51), residues: 91
  loop : -1.35 (0.28), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 747 
 TYR   0.011   0.001   TYR A 771 
 PHE   0.028   0.002   PHE A1372 
 TRP   0.019   0.002   TRP A 341 
 HIS   0.012   0.001   HIS A 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (11701)
  covalent geometry    : angle       0.62723 (16300)
  hydrogen bonds       : bond        0.05351 (  570)
  hydrogen bonds       : angle       4.69672 ( 1574)

*********************** 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
  77 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.390 
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  291 MET cc_start: 0.6834 (mmm) cc_final: 0.6265 (mpp)
REVERT: A  474 LEU cc_start: 0.9339 (mm) cc_final: 0.9052 (pp)
REVERT: A  773 LEU cc_start: 0.9191 (mt) cc_final: 0.8957 (mt)
REVERT: A  794 GLU cc_start: 0.9399 (OUTLIER) cc_final: 0.9178 (pp20)
REVERT: A  865 MET cc_start: 0.7606 (pmm) cc_final: 0.6648 (tpt)
REVERT: A 1026 MET cc_start: 0.8969 (mpp) cc_final: 0.8763 (mpp)
REVERT: A 1408 MET cc_start: 0.9746 (mtm) cc_final: 0.9446 (mtp)
REVERT: A 1412 MET cc_start: 0.8148 (mtm) cc_final: 0.7916 (mtp)
REVERT: A 1416 MET cc_start: 0.8818 (mmt) cc_final: 0.8289 (mmm)
REVERT: A 1637 PHE cc_start: 0.9760 (m-80) cc_final: 0.9553 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1013
  time to fit residues: 11.5617
Evaluate side-chains
  63 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 90 optimal weight:   40.0000
   chunk 48 optimal weight:    7.9990
   chunk 82 optimal weight:    0.1980
   chunk 115 optimal weight:   30.0000
   chunk 97 optimal weight:    7.9990
   chunk 67 optimal weight:   20.0000
   chunk 108 optimal weight:   10.0000
   chunk 73 optimal weight:   20.0000
   chunk 32 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    5.0386

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

Flipped N/Q/H residues before XYZ refinement:
A 253 GLN
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1606 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.042860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.032547 restraints weight = 180681.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.033083 restraints weight = 144926.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.033470 restraints weight = 122856.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.033757 restraints weight = 108825.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.033969 restraints weight = 99353.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.5693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11701  Z= 0.154
  Angle     :  0.649   8.276  16300  Z= 0.342
  Chirality :  0.039   0.249   1961
  Planarity :  0.005   0.089   1664
  Dihedral  : 21.432 171.971   2889
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 22.54
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.41 %
    Favored  : 95.23 %
  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:  0.41 (0.25), residues: 1111
  helix:  1.46 (0.20), residues: 613
  sheet: -0.70 (0.52), residues: 93
  loop : -1.35 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 694 
 TYR   0.020   0.002   TYR A1593 
 PHE   0.020   0.002   PHE A 846 
 TRP   0.020   0.002   TRP A1528 
 HIS   0.009   0.001   HIS A 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (11701)
  covalent geometry    : angle       0.64950 (16300)
  hydrogen bonds       : bond        0.05943 (  570)
  hydrogen bonds       : angle       4.84664 ( 1574)

*********************** 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
  76 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.296 
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  291 MET cc_start: 0.6780 (mmm) cc_final: 0.6184 (mpp)
REVERT: A  474 LEU cc_start: 0.9317 (mm) cc_final: 0.9009 (pp)
REVERT: A  556 PHE cc_start: 0.9181 (m-10) cc_final: 0.8835 (m-10)
REVERT: A 1026 MET cc_start: 0.8935 (mpp) cc_final: 0.8679 (mpp)
REVERT: A 1408 MET cc_start: 0.9743 (mtm) cc_final: 0.9452 (mtp)
REVERT: A 1412 MET cc_start: 0.8268 (mtm) cc_final: 0.8025 (mtp)
REVERT: A 1416 MET cc_start: 0.8850 (mmt) cc_final: 0.8320 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1039
  time to fit residues: 11.8125
Evaluate side-chains
  62 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 119 optimal weight:   30.0000
   chunk 42 optimal weight:    8.9990
   chunk 11 optimal weight:    0.0970
   chunk 122 optimal weight:   50.0000
   chunk 27 optimal weight:   10.0000
   chunk 3 optimal weight:    0.7980
   chunk 5 optimal weight:    9.9990
   chunk 74 optimal weight:   40.0000
   chunk 6 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0570
   chunk 77 optimal weight:    0.8980
   overall best weight:    1.5698

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.044649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.034077 restraints weight = 176337.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.034667 restraints weight = 140363.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.035092 restraints weight = 118236.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.035409 restraints weight = 104206.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.035659 restraints weight = 94710.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.5773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11701  Z= 0.122
  Angle     :  0.611   7.893  16300  Z= 0.320
  Chirality :  0.038   0.236   1961
  Planarity :  0.004   0.077   1664
  Dihedral  : 21.045 173.061   2889
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 17.68
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  3.33 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  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:  0.55 (0.25), residues: 1111
  helix:  1.56 (0.21), residues: 613
  sheet: -0.49 (0.54), residues: 91
  loop : -1.30 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 317 
 TYR   0.015   0.001   TYR A1649 
 PHE   0.034   0.002   PHE A1372 
 TRP   0.013   0.001   TRP A 341 
 HIS   0.005   0.001   HIS A 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (11701)
  covalent geometry    : angle       0.61130 (16300)
  hydrogen bonds       : bond        0.04847 (  570)
  hydrogen bonds       : angle       4.63546 ( 1574)

*********************** 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
  77 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  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: A  474 LEU cc_start: 0.9356 (mm) cc_final: 0.9060 (pp)
REVERT: A  579 LEU cc_start: 0.9744 (tt) cc_final: 0.9502 (mm)
REVERT: A  865 MET cc_start: 0.7523 (pmm) cc_final: 0.6545 (tpt)
REVERT: A 1026 MET cc_start: 0.8970 (mpp) cc_final: 0.8721 (mpp)
REVERT: A 1063 LEU cc_start: 0.9525 (tp) cc_final: 0.9142 (tt)
REVERT: A 1064 MET cc_start: 0.8909 (mmm) cc_final: 0.8213 (mmm)
REVERT: A 1408 MET cc_start: 0.9762 (mtm) cc_final: 0.9462 (mtp)
REVERT: A 1412 MET cc_start: 0.8259 (mtm) cc_final: 0.8029 (mtp)
REVERT: A 1416 MET cc_start: 0.8826 (mmt) cc_final: 0.8327 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.0971
  time to fit residues: 11.2812
Evaluate side-chains
  59 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 116 optimal weight:   20.0000
   chunk 119 optimal weight:   30.0000
   chunk 94 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 82 optimal weight:    7.9990
   chunk 110 optimal weight:    9.9990
   chunk 87 optimal weight:    7.9990
   chunk 40 optimal weight:   40.0000
   chunk 121 optimal weight:   40.0000
   overall best weight:    4.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1328 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.042717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.032465 restraints weight = 182278.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.033013 restraints weight = 146257.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.033407 restraints weight = 123807.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.033707 restraints weight = 109328.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.033907 restraints weight = 99531.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.6267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11701  Z= 0.141
  Angle     :  0.627   8.206  16300  Z= 0.328
  Chirality :  0.038   0.210   1961
  Planarity :  0.005   0.079   1664
  Dihedral  : 21.130 172.541   2889
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 21.94
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.50 %
    Favored  : 95.14 %
  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:  0.44 (0.25), residues: 1111
  helix:  1.54 (0.21), residues: 613
  sheet: -0.74 (0.54), residues: 93
  loop : -1.43 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 747 
 TYR   0.014   0.001   TYR A1514 
 PHE   0.023   0.002   PHE A 846 
 TRP   0.017   0.002   TRP A1528 
 HIS   0.004   0.001   HIS A 868 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11701)
  covalent geometry    : angle       0.62744 (16300)
  hydrogen bonds       : bond        0.05525 (  570)
  hydrogen bonds       : angle       4.71485 ( 1574)

*********************** 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
  74 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  474 LEU cc_start: 0.9319 (mm) cc_final: 0.8987 (pp)
REVERT: A 1026 MET cc_start: 0.9020 (mpp) cc_final: 0.8795 (mpp)
REVERT: A 1380 LEU cc_start: 0.9093 (tt) cc_final: 0.8863 (tp)
REVERT: A 1408 MET cc_start: 0.9743 (mtm) cc_final: 0.9429 (mtp)
REVERT: A 1416 MET cc_start: 0.8834 (mmt) cc_final: 0.8294 (mmm)
REVERT: A 1732 MET cc_start: 0.9568 (tpt) cc_final: 0.9355 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0857
  time to fit residues: 9.7695
Evaluate side-chains
  56 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 95 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 16 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 103 optimal weight:   20.0000
   chunk 63 optimal weight:   30.0000
   chunk 5 optimal weight:    6.9990
   chunk 78 optimal weight:    9.9990
   chunk 112 optimal weight:   30.0000
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1399 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.040476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.030535 restraints weight = 187424.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.031046 restraints weight = 148797.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.031431 restraints weight = 125756.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.031707 restraints weight = 111024.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.031895 restraints weight = 101028.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.7038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11701  Z= 0.188
  Angle     :  0.698   8.373  16300  Z= 0.366
  Chirality :  0.040   0.208   1961
  Planarity :  0.005   0.087   1664
  Dihedral  : 21.535 172.362   2889
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 28.33
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  5.58 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  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: -0.02 (0.25), residues: 1111
  helix:  1.18 (0.21), residues: 613
  sheet: -0.87 (0.55), residues: 84
  loop : -1.65 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 747 
 TYR   0.017   0.002   TYR A1593 
 PHE   0.025   0.002   PHE A 785 
 TRP   0.034   0.003   TRP A1528 
 HIS   0.006   0.001   HIS A 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (11701)
  covalent geometry    : angle       0.69759 (16300)
  hydrogen bonds       : bond        0.06578 (  570)
  hydrogen bonds       : angle       5.10600 ( 1574)

*********************** 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
  71 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.287 
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  291 MET cc_start: 0.6511 (mpp) cc_final: 0.5883 (mpp)
REVERT: A  375 LEU cc_start: 0.9482 (tp) cc_final: 0.9142 (tp)
REVERT: A  774 MET cc_start: 0.8177 (mpp) cc_final: 0.7891 (mpp)
REVERT: A 1380 LEU cc_start: 0.9194 (tt) cc_final: 0.8924 (tp)
REVERT: A 1408 MET cc_start: 0.9757 (mtm) cc_final: 0.9421 (mtp)
REVERT: A 1412 MET cc_start: 0.8269 (mtm) cc_final: 0.8017 (ptp)
REVERT: A 1416 MET cc_start: 0.8838 (mmt) cc_final: 0.8351 (mmm)
REVERT: A 1732 MET cc_start: 0.9561 (tpt) cc_final: 0.9348 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0954
  time to fit residues: 10.1671
Evaluate side-chains
  56 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 61 optimal weight:   30.0000
   chunk 13 optimal weight:    0.9990
   chunk 119 optimal weight:   30.0000
   chunk 43 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 100 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 107 optimal weight:    8.9990
   chunk 96 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
A 788 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.041754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.031697 restraints weight = 181521.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.032232 restraints weight = 144205.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.032602 restraints weight = 121906.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.032905 restraints weight = 108148.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.033109 restraints weight = 98162.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.7041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11701  Z= 0.138
  Angle     :  0.645   8.247  16300  Z= 0.337
  Chirality :  0.039   0.198   1961
  Planarity :  0.004   0.077   1664
  Dihedral  : 21.312 173.104   2889
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 21.75
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.50 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  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:  0.13 (0.25), residues: 1111
  helix:  1.32 (0.21), residues: 611
  sheet: -1.02 (0.52), residues: 93
  loop : -1.56 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 747 
 TYR   0.013   0.001   TYR A1514 
 PHE   0.019   0.002   PHE A 785 
 TRP   0.027   0.002   TRP A1528 
 HIS   0.007   0.001   HIS A 381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (11701)
  covalent geometry    : angle       0.64503 (16300)
  hydrogen bonds       : bond        0.05311 (  570)
  hydrogen bonds       : angle       4.94517 ( 1574)

*********************** 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
  73 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.387 
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: A  291 MET cc_start: 0.6438 (mpp) cc_final: 0.5797 (mpp)
REVERT: A  548 CYS cc_start: 0.9237 (t) cc_final: 0.8594 (p)
REVERT: A  737 LEU cc_start: 0.7687 (pt) cc_final: 0.7472 (mt)
REVERT: A 1026 MET cc_start: 0.8926 (mpp) cc_final: 0.8694 (mpp)
REVERT: A 1380 LEU cc_start: 0.9139 (tt) cc_final: 0.8913 (tp)
REVERT: A 1408 MET cc_start: 0.9748 (mtm) cc_final: 0.9479 (mtp)
REVERT: A 1412 MET cc_start: 0.8122 (mtm) cc_final: 0.7864 (mtp)
REVERT: A 1416 MET cc_start: 0.8795 (mmt) cc_final: 0.8247 (mmm)
REVERT: A 1732 MET cc_start: 0.9602 (tpt) cc_final: 0.9361 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0900
  time to fit residues: 10.1697
Evaluate side-chains
  58 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 109 optimal weight:   50.0000
   chunk 26 optimal weight:    5.9990
   chunk 30 optimal weight:    0.4980
   chunk 49 optimal weight:    8.9990
   chunk 21 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   chunk 115 optimal weight:   30.0000
   chunk 103 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    5.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.040878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.030931 restraints weight = 184794.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.031476 restraints weight = 146388.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.031874 restraints weight = 122581.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.032158 restraints weight = 107792.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.032352 restraints weight = 97992.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.7348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11701  Z= 0.158
  Angle     :  0.668   9.085  16300  Z= 0.350
  Chirality :  0.039   0.201   1961
  Planarity :  0.005   0.079   1664
  Dihedral  : 21.363 172.707   2889
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 24.11
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  5.40 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  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:  0.03 (0.25), residues: 1111
  helix:  1.23 (0.21), residues: 611
  sheet: -1.01 (0.54), residues: 89
  loop : -1.60 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 747 
 TYR   0.014   0.001   TYR A1514 
 PHE   0.021   0.002   PHE A 785 
 TRP   0.034   0.002   TRP A1528 
 HIS   0.005   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (11701)
  covalent geometry    : angle       0.66752 (16300)
  hydrogen bonds       : bond        0.05951 (  570)
  hydrogen bonds       : angle       5.05781 ( 1574)

********************** 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
  73 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 MET cc_start: 0.6270 (mpp) cc_final: 0.5596 (mpp)
REVERT: A 1026 MET cc_start: 0.8993 (mpp) cc_final: 0.8752 (mpp)
REVERT: A 1380 LEU cc_start: 0.9127 (tt) cc_final: 0.8887 (tp)
REVERT: A 1408 MET cc_start: 0.9739 (mtm) cc_final: 0.9463 (mtp)
REVERT: A 1412 MET cc_start: 0.8160 (mtm) cc_final: 0.7928 (mtp)
REVERT: A 1416 MET cc_start: 0.8767 (mmt) cc_final: 0.8265 (mmm)
REVERT: A 1526 MET cc_start: 0.9232 (tmm) cc_final: 0.9010 (tmm)
REVERT: A 1732 MET cc_start: 0.9605 (tpt) cc_final: 0.9338 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0903
  time to fit residues: 10.3388
Evaluate side-chains
  55 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 106 optimal weight:    0.6980
   chunk 6 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 115 optimal weight:   30.0000
   chunk 34 optimal weight:   10.0000
   chunk 0 optimal weight:   50.0000
   chunk 31 optimal weight:    9.9990
   chunk 72 optimal weight:   40.0000
   chunk 65 optimal weight:    9.9990
   chunk 66 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    6.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
A 333 GLN
A 398 HIS
A1669 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.039598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.029854 restraints weight = 189089.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.030364 restraints weight = 148878.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.030750 restraints weight = 125693.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.031027 restraints weight = 110583.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.031165 restraints weight = 100312.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.7961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11701  Z= 0.190
  Angle     :  0.726   9.323  16300  Z= 0.380
  Chirality :  0.041   0.222   1961
  Planarity :  0.005   0.088   1664
  Dihedral  : 21.602 172.425   2889
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 29.62
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  6.03 %
    Favored  : 93.52 %
  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 : 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: -0.29 (0.25), residues: 1111
  helix:  0.94 (0.21), residues: 617
  sheet: -1.14 (0.53), residues: 89
  loop : -1.73 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 405 
 TYR   0.015   0.002   TYR A1514 
 PHE   0.023   0.003   PHE A 785 
 TRP   0.043   0.003   TRP A1528 
 HIS   0.006   0.001   HIS A 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (11701)
  covalent geometry    : angle       0.72560 (16300)
  hydrogen bonds       : bond        0.06602 (  570)
  hydrogen bonds       : angle       5.26625 ( 1574)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2225.10 seconds
wall clock time: 39 minutes 17.14 seconds (2357.14 seconds total)