Starting phenix.real_space_refine
on Tue Jul 29 14:29:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7eld_31181/07_2025/7eld_31181.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eld_31181/07_2025/7eld_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7eld_31181/07_2025/7eld_31181.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eld_31181/07_2025/7eld_31181.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eld_31181/07_2025/7eld_31181.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eld_31181/07_2025/7eld_31181.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.74, per 1000 atoms: 0.60
  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: 2.50
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 4.42
  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: 6.20

  Time building geometry restraints manager: 3.03 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:             0.600
  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:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     32.450
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.520
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.009   0.001   TRP A 547 
 HIS   0.009   0.001   HIS A 387 
 PHE   0.010   0.001   PHE A1613 
 TYR   0.011   0.002   TYR A 757 
 ARG   0.005   0.001   ARG A1062 

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

*********************** 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  : 1.047 
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: 0.8296 (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: 0.2518
  time to fit residues: 77.1456
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  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    9.9990
   chunk 93 optimal weight:    7.9990
   chunk 51 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 49 optimal weight:    8.9990
   chunk 96 optimal weight:    8.9990
   chunk 37 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   chunk 71 optimal weight:   20.0000
   chunk 111 optimal weight:   20.0000
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 326 HIS
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
A1739 GLN
** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.044689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.034195 restraints weight = 175744.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.034762 restraints weight = 140285.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.035146 restraints weight = 118460.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.4134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11701  Z= 0.226
  Angle     :  0.785   8.884  16300  Z= 0.416
  Chirality :  0.043   0.218   1961
  Planarity :  0.005   0.079   1664
  Dihedral  : 21.860 171.021   2889
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 28.28
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  2.61 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  3.66 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.24), residues: 1111
  helix:  1.91 (0.19), residues: 622
  sheet: -0.34 (0.56), residues: 76
  loop : -1.15 (0.27), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP A1528 
 HIS   0.011   0.002   HIS A1401 
 PHE   0.022   0.003   PHE A 785 
 TYR   0.032   0.003   TYR A1513 
 ARG   0.011   0.001   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06927 (  570)
  hydrogen bonds       : angle       5.11330 ( 1574)
  covalent geometry    : bond        0.00446 (11701)
  covalent geometry    : angle       0.78507 (16300)

*********************** 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
  89 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 1.146 
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  474 LEU cc_start: 0.9303 (mm) cc_final: 0.9040 (pp)
REVERT: A  712 MET cc_start: 0.9603 (ttm) cc_final: 0.9387 (mpp)
REVERT: A  865 MET cc_start: 0.7523 (pmm) cc_final: 0.6770 (tpp)
REVERT: A 1408 MET cc_start: 0.9741 (mtm) cc_final: 0.9441 (mtp)
REVERT: A 1416 MET cc_start: 0.8754 (mmt) cc_final: 0.8235 (mmm)
REVERT: A 1637 PHE cc_start: 0.9612 (m-10) cc_final: 0.9376 (m-10)
  outliers start: 4
  outliers final: 1
  residues processed: 89
  average time/residue: 0.2849
  time to fit residues: 35.6622
Evaluate side-chains
  64 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 98 optimal weight:    7.9990
   chunk 71 optimal weight:   40.0000
   chunk 56 optimal weight:   20.0000
   chunk 102 optimal weight:   10.0000
   chunk 18 optimal weight:   20.0000
   chunk 7 optimal weight:    8.9990
   chunk 91 optimal weight:    5.9990
   chunk 89 optimal weight:   20.0000
   overall best weight:    4.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 287 HIS
A 293 GLN
A 433 ASN
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 984 HIS
A1582 HIS
A1606 HIS
** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.044372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.033780 restraints weight = 177201.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.034399 restraints weight = 138392.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.034845 restraints weight = 115066.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.4665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11701  Z= 0.153
  Angle     :  0.666   8.884  16300  Z= 0.349
  Chirality :  0.040   0.210   1961
  Planarity :  0.005   0.094   1664
  Dihedral  : 21.791 172.256   2889
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 21.15
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  3.42 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.17 %
    Favored  : 95.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.24), residues: 1111
  helix:  1.68 (0.20), residues: 613
  sheet: -0.50 (0.52), residues: 91
  loop : -1.27 (0.28), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 341 
 HIS   0.004   0.001   HIS A 868 
 PHE   0.019   0.002   PHE A 785 
 TYR   0.014   0.002   TYR A1593 
 ARG   0.009   0.001   ARG A 747 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05754 (  570)
  hydrogen bonds       : angle       4.88291 ( 1574)
  covalent geometry    : bond        0.00302 (11701)
  covalent geometry    : angle       0.66565 (16300)

*********************** 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
  83 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 1.079 
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  369 MET cc_start: 0.4303 (mtp) cc_final: 0.4058 (mtp)
REVERT: A  474 LEU cc_start: 0.9397 (mm) cc_final: 0.9119 (pp)
REVERT: A  684 PHE cc_start: 0.9273 (m-80) cc_final: 0.8896 (m-80)
REVERT: A  773 LEU cc_start: 0.9173 (mt) cc_final: 0.8972 (mt)
REVERT: A  865 MET cc_start: 0.7649 (pmm) cc_final: 0.6651 (tpp)
REVERT: A 1026 MET cc_start: 0.8930 (mpp) cc_final: 0.8651 (mpp)
REVERT: A 1201 MET cc_start: 0.8456 (tpt) cc_final: 0.8228 (tpp)
REVERT: A 1408 MET cc_start: 0.9762 (mtm) cc_final: 0.9485 (mtp)
REVERT: A 1412 MET cc_start: 0.8170 (mtm) cc_final: 0.7863 (mtp)
REVERT: A 1416 MET cc_start: 0.8804 (mmt) cc_final: 0.8290 (mmm)
REVERT: A 1637 PHE cc_start: 0.9620 (m-10) cc_final: 0.9373 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 83
  average time/residue: 0.2409
  time to fit residues: 29.2454
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  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 102 optimal weight:    8.9990
   chunk 114 optimal weight:   40.0000
   chunk 36 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 57 optimal weight:   20.0000
   chunk 37 optimal weight:    8.9990
   chunk 80 optimal weight:   20.0000
   chunk 69 optimal weight:    9.9990
   chunk 44 optimal weight:    8.9990
   chunk 71 optimal weight:   20.0000
   chunk 88 optimal weight:    2.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1399 GLN
** A1776 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 = 0.3396 r_free = 0.3396 target = 0.042410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.032150 restraints weight = 180875.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.032656 restraints weight = 145049.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.033044 restraints weight = 123508.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.5461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11701  Z= 0.172
  Angle     :  0.676   8.739  16300  Z= 0.356
  Chirality :  0.040   0.216   1961
  Planarity :  0.005   0.099   1664
  Dihedral  : 21.802 171.774   2889
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 26.34
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  3.96 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.24), residues: 1111
  helix:  1.41 (0.20), residues: 613
  sheet: -0.69 (0.51), residues: 93
  loop : -1.45 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A1528 
 HIS   0.014   0.002   HIS A 287 
 PHE   0.033   0.002   PHE A1372 
 TYR   0.013   0.002   TYR A1514 
 ARG   0.007   0.001   ARG A1788 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06431 (  570)
  hydrogen bonds       : angle       4.97267 ( 1574)
  covalent geometry    : bond        0.00340 (11701)
  covalent geometry    : angle       0.67634 (16300)

*********************** 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
  70 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.141 
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: 0.9329 (mm) cc_final: 0.9016 (pp)
REVERT: A  773 LEU cc_start: 0.9166 (mt) cc_final: 0.8939 (mt)
REVERT: A  865 MET cc_start: 0.7613 (pmm) cc_final: 0.6573 (tpp)
REVERT: A 1026 MET cc_start: 0.8931 (mpp) cc_final: 0.8684 (mpp)
REVERT: A 1201 MET cc_start: 0.8405 (tpt) cc_final: 0.8195 (tpp)
REVERT: A 1385 LEU cc_start: 0.9626 (tp) cc_final: 0.9392 (mm)
REVERT: A 1408 MET cc_start: 0.9740 (mtm) cc_final: 0.9441 (mtp)
REVERT: A 1412 MET cc_start: 0.8124 (mtm) cc_final: 0.7808 (mtp)
REVERT: A 1416 MET cc_start: 0.8883 (mmt) cc_final: 0.8361 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.2425
  time to fit residues: 25.5417
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  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 39 optimal weight:   30.0000
   chunk 78 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 76 optimal weight:    0.2980
   chunk 12 optimal weight:    3.9990
   chunk 77 optimal weight:    8.9990
   chunk 101 optimal weight:   20.0000
   overall best weight:    3.8588

-------------------------------------------------------------------------------
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 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.042816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.032451 restraints weight = 180287.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.033026 restraints weight = 144866.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.033417 restraints weight = 121544.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.5719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11701  Z= 0.139
  Angle     :  0.637   9.253  16300  Z= 0.331
  Chirality :  0.039   0.258   1961
  Planarity :  0.005   0.090   1664
  Dihedral  : 21.567 172.720   2889
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 21.24
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.14 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.85 %
    Favored  : 96.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1111
  helix:  1.44 (0.20), residues: 614
  sheet: -0.72 (0.52), residues: 93
  loop : -1.40 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 341 
 HIS   0.009   0.001   HIS A 287 
 PHE   0.019   0.002   PHE A 846 
 TYR   0.017   0.002   TYR A1255 
 ARG   0.006   0.001   ARG A1788 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05508 (  570)
  hydrogen bonds       : angle       4.84916 ( 1574)
  covalent geometry    : bond        0.00277 (11701)
  covalent geometry    : angle       0.63669 (16300)

*********************** 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
  75 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 1.419 
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: 0.6695 (mmm) cc_final: 0.5552 (mpp)
REVERT: A  474 LEU cc_start: 0.9309 (mm) cc_final: 0.8987 (pp)
REVERT: A  865 MET cc_start: 0.7598 (pmm) cc_final: 0.6591 (tpp)
REVERT: A 1026 MET cc_start: 0.8965 (mpp) cc_final: 0.8625 (mpp)
REVERT: A 1408 MET cc_start: 0.9746 (mtm) cc_final: 0.9450 (mtp)
REVERT: A 1412 MET cc_start: 0.8204 (mtm) cc_final: 0.7994 (mtp)
REVERT: A 1416 MET cc_start: 0.8912 (mmt) cc_final: 0.8406 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 75
  average time/residue: 0.2479
  time to fit residues: 28.0354
Evaluate side-chains
  54 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 90 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 52 optimal weight:   40.0000
   chunk 14 optimal weight:    7.9990
   chunk 67 optimal weight:    6.9990
   chunk 77 optimal weight:    9.9990
   chunk 101 optimal weight:   30.0000
   chunk 98 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 253 GLN
** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1420 GLN
** A1776 ASN ** 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 = 0.3397 r_free = 0.3397 target = 0.042571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.032255 restraints weight = 183014.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.032792 restraints weight = 145654.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.033204 restraints weight = 123096.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.6013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11701  Z= 0.139
  Angle     :  0.630   8.249  16300  Z= 0.329
  Chirality :  0.038   0.232   1961
  Planarity :  0.005   0.086   1664
  Dihedral  : 21.404 172.629   2889
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 21.71
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.68 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.73 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.25), residues: 1111
  helix:  1.43 (0.20), residues: 614
  sheet: -0.81 (0.53), residues: 93
  loop : -1.51 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 547 
 HIS   0.007   0.001   HIS A 287 
 PHE   0.038   0.002   PHE A1372 
 TYR   0.013   0.001   TYR A1649 
 ARG   0.007   0.001   ARG A1788 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05380 (  570)
  hydrogen bonds       : angle       4.82069 ( 1574)
  covalent geometry    : bond        0.00277 (11701)
  covalent geometry    : angle       0.62955 (16300)

*********************** 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
  72 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 1.159 
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: 0.6348 (mmm) cc_final: 0.6036 (mpp)
REVERT: A  474 LEU cc_start: 0.9326 (mm) cc_final: 0.8998 (pp)
REVERT: A  712 MET cc_start: 0.9344 (mmp) cc_final: 0.9138 (mmm)
REVERT: A  794 GLU cc_start: 0.9486 (OUTLIER) cc_final: 0.9185 (pp20)
REVERT: A  865 MET cc_start: 0.7664 (pmm) cc_final: 0.6607 (mmm)
REVERT: A 1026 MET cc_start: 0.8928 (mpp) cc_final: 0.8536 (mpp)
REVERT: A 1408 MET cc_start: 0.9746 (mtm) cc_final: 0.9446 (mtp)
REVERT: A 1416 MET cc_start: 0.8930 (mmt) cc_final: 0.8408 (mmm)
REVERT: A 1526 MET cc_start: 0.9233 (tmm) cc_final: 0.8972 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 72
  average time/residue: 0.2708
  time to fit residues: 29.1373
Evaluate side-chains
  56 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 95 optimal weight:   20.0000
   chunk 73 optimal weight:   30.0000
   chunk 29 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 75 optimal weight:   30.0000
   chunk 57 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
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 333 GLN
** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 398 HIS
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 808 HIS
A1328 GLN
** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.040061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.030106 restraints weight = 191211.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.030615 restraints weight = 151753.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.030987 restraints weight = 128319.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.6909

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= 0.195
  Angle     :  0.711   8.350  16300  Z= 0.373
  Chirality :  0.041   0.224   1961
  Planarity :  0.005   0.095   1664
  Dihedral  : 21.772 172.452   2889
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 30.59
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.40 %
    Favored  : 94.24 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.25), residues: 1111
  helix:  1.04 (0.21), residues: 619
  sheet: -1.12 (0.52), residues: 93
  loop : -1.72 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A 547 
 HIS   0.007   0.002   HIS A 381 
 PHE   0.034   0.003   PHE A1372 
 TYR   0.014   0.002   TYR A 327 
 ARG   0.011   0.001   ARG A 747 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06844 (  570)
  hydrogen bonds       : angle       5.20131 ( 1574)
  covalent geometry    : bond        0.00385 (11701)
  covalent geometry    : angle       0.71062 (16300)

*********************** 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
  70 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.196 
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: 0.6357 (mmm) cc_final: 0.6052 (mpp)
REVERT: A  712 MET cc_start: 0.9375 (mmp) cc_final: 0.9151 (mmm)
REVERT: A  774 MET cc_start: 0.8037 (mpp) cc_final: 0.7514 (mpp)
REVERT: A  865 MET cc_start: 0.7626 (pmm) cc_final: 0.6526 (tpt)
REVERT: A 1026 MET cc_start: 0.8906 (mpp) cc_final: 0.8465 (mpp)
REVERT: A 1408 MET cc_start: 0.9765 (mtm) cc_final: 0.9494 (mtp)
REVERT: A 1412 MET cc_start: 0.8113 (mtm) cc_final: 0.7874 (mtp)
REVERT: A 1416 MET cc_start: 0.8860 (mmt) cc_final: 0.8383 (mmm)
REVERT: A 1526 MET cc_start: 0.9294 (tmm) cc_final: 0.9086 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.2534
  time to fit residues: 26.5297
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  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 86 optimal weight:   20.0000
   chunk 72 optimal weight:   20.0000
   chunk 99 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 62 optimal weight:   30.0000
   chunk 78 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 103 optimal weight:   20.0000
   overall best weight:    4.1788

-------------------------------------------------------------------------------
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 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1718 GLN
** A1776 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 = 0.3368 r_free = 0.3368 target = 0.041243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.031184 restraints weight = 185342.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.031725 restraints weight = 147198.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.032125 restraints weight = 123688.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.6894

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= 0.141
  Angle     :  0.641   8.715  16300  Z= 0.334
  Chirality :  0.039   0.206   1961
  Planarity :  0.005   0.084   1664
  Dihedral  : 21.473 173.217   2889
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 23.60
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.59 %
    Favored  : 94.96 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.25), residues: 1111
  helix:  1.22 (0.21), residues: 613
  sheet: -1.15 (0.52), residues: 96
  loop : -1.61 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A1528 
 HIS   0.007   0.001   HIS A1611 
 PHE   0.020   0.002   PHE A 785 
 TYR   0.012   0.001   TYR A1649 
 ARG   0.016   0.001   ARG A1788 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05354 (  570)
  hydrogen bonds       : angle       4.99062 ( 1574)
  covalent geometry    : bond        0.00277 (11701)
  covalent geometry    : angle       0.64123 (16300)

*********************** 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
  72 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 1.589 
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  548 CYS cc_start: 0.9382 (t) cc_final: 0.8382 (p)
REVERT: A  737 LEU cc_start: 0.7385 (pt) cc_final: 0.7174 (mt)
REVERT: A  774 MET cc_start: 0.8010 (mpp) cc_final: 0.7659 (mpp)
REVERT: A  865 MET cc_start: 0.7556 (pmm) cc_final: 0.6570 (tpt)
REVERT: A 1026 MET cc_start: 0.8922 (mpp) cc_final: 0.8508 (mpp)
REVERT: A 1408 MET cc_start: 0.9763 (mtm) cc_final: 0.9488 (mtp)
REVERT: A 1412 MET cc_start: 0.8021 (mtm) cc_final: 0.7805 (mtp)
REVERT: A 1416 MET cc_start: 0.8848 (mmt) cc_final: 0.8324 (mmm)
REVERT: A 1526 MET cc_start: 0.9315 (tmm) cc_final: 0.9089 (tmm)
REVERT: A 1732 MET cc_start: 0.9585 (tpt) cc_final: 0.9380 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.3316
  time to fit residues: 36.8667
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  : 1.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 77 optimal weight:    0.0040
   chunk 112 optimal weight:   50.0000
   chunk 71 optimal weight:    3.9990
   chunk 0 optimal weight:   50.0000
   chunk 21 optimal weight:   10.0000
   chunk 2 optimal weight:   20.0000
   chunk 59 optimal weight:    9.9990
   chunk 105 optimal weight:   20.0000
   chunk 61 optimal weight:    0.0050
   chunk 83 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   overall best weight:    4.0012

-------------------------------------------------------------------------------
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
** A1776 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 = 0.3362 r_free = 0.3362 target = 0.041132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.031157 restraints weight = 184896.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.031702 restraints weight = 146817.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.032081 restraints weight = 123274.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
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      :  0.003   0.028  11701  Z= 0.141
  Angle     :  0.639   8.955  16300  Z= 0.332
  Chirality :  0.038   0.198   1961
  Planarity :  0.005   0.082   1664
  Dihedral  : 21.368 173.054   2889
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 23.51
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.59 %
    Favored  : 94.96 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.25), residues: 1111
  helix:  1.24 (0.21), residues: 613
  sheet: -1.17 (0.53), residues: 96
  loop : -1.62 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A1528 
 HIS   0.004   0.001   HIS A 287 
 PHE   0.026   0.002   PHE A 556 
 TYR   0.013   0.001   TYR A 550 
 ARG   0.008   0.001   ARG A1788 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05401 (  570)
  hydrogen bonds       : angle       5.01192 ( 1574)
  covalent geometry    : bond        0.00280 (11701)
  covalent geometry    : angle       0.63851 (16300)

*********************** 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
  71 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.4290 (mtp) cc_final: 0.3982 (mtp)
REVERT: A  548 CYS cc_start: 0.9346 (t) cc_final: 0.8388 (p)
REVERT: A  712 MET cc_start: 0.9273 (mmp) cc_final: 0.9040 (mmm)
REVERT: A  737 LEU cc_start: 0.7428 (pt) cc_final: 0.7227 (mt)
REVERT: A  774 MET cc_start: 0.8059 (mpp) cc_final: 0.7656 (mpp)
REVERT: A  865 MET cc_start: 0.7537 (pmm) cc_final: 0.6528 (tpt)
REVERT: A 1026 MET cc_start: 0.8948 (mpp) cc_final: 0.8533 (mpp)
REVERT: A 1408 MET cc_start: 0.9770 (mtm) cc_final: 0.9482 (mtp)
REVERT: A 1412 MET cc_start: 0.8041 (mtm) cc_final: 0.7816 (mtp)
REVERT: A 1416 MET cc_start: 0.8832 (mmt) cc_final: 0.8295 (mmm)
REVERT: A 1526 MET cc_start: 0.9322 (tmm) cc_final: 0.9093 (tmm)
REVERT: A 1732 MET cc_start: 0.9608 (tpt) cc_final: 0.9400 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.3205
  time to fit residues: 33.7377
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  : 1.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 92 optimal weight:   20.0000
   chunk 71 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   chunk 43 optimal weight:    9.9990
   chunk 85 optimal weight:   20.0000
   chunk 94 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 52 optimal weight:   30.0000
   chunk 106 optimal weight:    0.0870
   chunk 70 optimal weight:   10.0000
   chunk 93 optimal weight:    5.9990
   overall best weight:    3.8166

-------------------------------------------------------------------------------
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
** A1776 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 = 0.3363 r_free = 0.3363 target = 0.041219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.031226 restraints weight = 183418.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.031745 restraints weight = 145881.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.032134 restraints weight = 123536.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.7268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11701  Z= 0.135
  Angle     :  0.628   8.912  16300  Z= 0.324
  Chirality :  0.038   0.199   1961
  Planarity :  0.005   0.077   1664
  Dihedral  : 21.187 173.200   2889
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 21.98
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.59 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.25), residues: 1111
  helix:  1.33 (0.21), residues: 613
  sheet: -0.92 (0.57), residues: 87
  loop : -1.64 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A1528 
 HIS   0.004   0.001   HIS A 398 
 PHE   0.019   0.002   PHE A 846 
 TYR   0.013   0.001   TYR A1514 
 ARG   0.006   0.001   ARG A1335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05207 (  570)
  hydrogen bonds       : angle       4.95000 ( 1574)
  covalent geometry    : bond        0.00269 (11701)
  covalent geometry    : angle       0.62817 (16300)

********************** 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
  75 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 1.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.4114 (mtp) cc_final: 0.3801 (mtp)
REVERT: A  737 LEU cc_start: 0.7556 (pt) cc_final: 0.7291 (mt)
REVERT: A  774 MET cc_start: 0.8062 (mpp) cc_final: 0.7628 (mpp)
REVERT: A  865 MET cc_start: 0.7602 (pmm) cc_final: 0.6653 (tpt)
REVERT: A 1026 MET cc_start: 0.8952 (mpp) cc_final: 0.8536 (mpp)
REVERT: A 1408 MET cc_start: 0.9765 (mtm) cc_final: 0.9472 (mtp)
REVERT: A 1416 MET cc_start: 0.8789 (mmt) cc_final: 0.8273 (mmm)
REVERT: A 1526 MET cc_start: 0.9315 (tmm) cc_final: 0.9067 (tmm)
REVERT: A 1732 MET cc_start: 0.9533 (tpt) cc_final: 0.9298 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.3501
  time to fit residues: 39.5079
Evaluate side-chains
  57 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 54 optimal weight:   50.0000
   chunk 101 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 111 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0170
   chunk 77 optimal weight:    0.5980
   chunk 16 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 121 optimal weight:   40.0000
   overall best weight:    2.3224

-------------------------------------------------------------------------------
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
** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.042076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.031952 restraints weight = 181489.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.032520 restraints weight = 141320.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.032938 restraints weight = 117745.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.7282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11701  Z= 0.123
  Angle     :  0.625   8.671  16300  Z= 0.322
  Chirality :  0.038   0.194   1961
  Planarity :  0.004   0.071   1664
  Dihedral  : 20.960 173.579   2889
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 18.79
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.59 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.25), residues: 1111
  helix:  1.34 (0.21), residues: 618
  sheet: -0.79 (0.57), residues: 87
  loop : -1.59 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A1528 
 HIS   0.003   0.001   HIS A 398 
 PHE   0.019   0.002   PHE A 846 
 TYR   0.012   0.001   TYR A1514 
 ARG   0.005   0.000   ARG A 747 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04849 (  570)
  hydrogen bonds       : angle       4.84147 ( 1574)
  covalent geometry    : bond        0.00245 (11701)
  covalent geometry    : angle       0.62527 (16300)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4862.73 seconds
wall clock time: 91 minutes 35.68 seconds (5495.68 seconds total)