Starting phenix.real_space_refine
on Tue Mar  3 16:42:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7swq_25482/03_2026/7swq_25482.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7swq_25482/03_2026/7swq_25482.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7swq_25482/03_2026/7swq_25482.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7swq_25482/03_2026/7swq_25482.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7swq_25482/03_2026/7swq_25482.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7swq_25482/03_2026/7swq_25482.map"
  }
  resolution = 3.79
  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=   0.003
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: 6
    Type Number    sf(0)   Gaussians
     P      35      5.49       5
     Mg      1      5.21       5
     S      37      5.16       5
     C    4310      2.51       5
     N    1238      2.21       5
     O    1377      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: 6998
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 791, 6280
          Classifications: {'peptide': 791}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 746}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 452
          Classifications: {'RNA': 21}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 10, 'rna3p_pyr': 5}
          Link IDs: {'rna2p': 6, 'rna3p': 14}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 265
          Classifications: {'DNA': 1, 'RNA': 13}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 2, 'rna3p': 11}
          Chain breaks: 1
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'  U%rna2p_pyr:plan': 1, '  A:plan': 1, '  A:plan2': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.84, per 1000 atoms: 0.26
  Number of scatterers: 6998
  At special positions: 0
  Unit cell: (83.72, 98.28, 111.93, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      37     16.00
     P      35     15.00
     Mg      1     11.99
     O    1377      8.00
     N    1238      7.00
     C    4310      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: 0.37
  Conformation dependent library (CDL) restraints added in 237.6 milliseconds
  

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
Warning! O6 atom is missing from residue    G B   2  
  Was trying to link:    C D  20 N4 with    G B   2 O6, Saenger class: 19
Warning! O6 atom is missing from residue    G B   2  
  Was trying to link:    C D  20 N4 with    G B   2 O6, Saenger class: 19
    Secondary structure from input PDB file:
      18 helices and 13 sheets defined
      29.8% alpha, 11.1% beta
      9 base pairs and 13 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 170 through 186
      removed outlier: 3.580A  pdb=" N   ALA A 176 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 283
    Processing helix  chain 'A' and resid 338 through 348
    Processing helix  chain 'A' and resid 357 through 369
    Processing helix  chain 'A' and resid 462 through 472
      removed outlier: 3.914A  pdb=" N   VAL A 470 " --> pdb=" O   ALA A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 490
      removed outlier: 3.652A  pdb=" N   VAL A 486 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 501
    Processing helix  chain 'A' and resid 565 through 583
      removed outlier: 3.617A  pdb=" N   ARG A 570 " --> pdb=" O   GLU A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 618
      removed outlier: 4.017A  pdb=" N   TYR A 611 " --> pdb=" O   LEU A 607 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   SER A 614 " --> pdb=" O   VAL A 610 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   MET A 615 " --> pdb=" O   TYR A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 645
    Processing helix  chain 'A' and resid 657 through 662
      removed outlier: 3.692A  pdb=" N   PHE A 662 " --> pdb=" O   THR A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 680
      removed outlier: 3.986A  pdb=" N   LEU A 674 " --> pdb=" O   ALA A 670 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS A 675 " --> pdb=" O   ASN A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 692
    Processing helix  chain 'A' and resid 775 through 784
    Processing helix  chain 'A' and resid 801 through 821
      removed outlier: 3.627A  pdb=" N   VAL A 805 " --> pdb=" O   GLN A 801 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU A 810 " --> pdb=" O   LEU A 806 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ILE A 813 " --> pdb=" O   GLU A 809 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ALA A 818 " --> pdb=" O   ARG A 814 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   SER A 819 " --> pdb=" O   LYS A 815 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU A 820 " --> pdb=" O   ALA A 816 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   GLU A 821 " --> pdb=" O   CYS A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 903 through 915
      removed outlier: 3.528A  pdb=" N   GLN A 908 " --> pdb=" O   ALA A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 928 through 945
      removed outlier: 4.089A  pdb=" N   ALA A 934 " --> pdb=" O   PRO A 930 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   HIS A 935 " --> pdb=" O   ALA A 931 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE A 939 " --> pdb=" O   HIS A 935 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ALA A 941 " --> pdb=" O   ALA A 937 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   ARG A 942 " --> pdb=" O   ALA A 938 " (cutoff:3.500A)
      removed outlier: 5.191A  pdb=" N   PHE A 943 " --> pdb=" O   PHE A 939 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   TYR A 944 " --> pdb=" O   ARG A 940 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 978 through 982
      removed outlier: 3.733A  pdb=" N   LYS A 982 " --> pdb=" O   GLU A 979 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 140
    Processing sheet with id=AA2, first strand: chain 'A' and resid 509 through 511
    Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 151
      removed outlier: 3.656A  pdb=" N   ASN A 503 " --> pdb=" O   ASP A 151 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 197
      removed outlier: 3.885A  pdb=" N   LYS A 242 " --> pdb=" O   ASP A 161 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 305 through 306
    Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 311
    Processing sheet with id=AA7, first strand: chain 'A' and resid 315 through 316
    Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 440
      removed outlier: 3.897A  pdb=" N   SER A 440 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   GLN A 432 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   ARG A 386 " --> pdb=" O   GLY A 434 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 531 through 532
      removed outlier: 4.132A  pdb=" N   VAL A 686 " --> pdb=" O   LYS A 522 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 556 through 559
    Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 705
      removed outlier: 6.424A  pdb=" N   ILE A 704 " --> pdb=" O   ILE A 791 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 710
    Processing sheet with id=AB4, first strand: chain 'A' and resid 829 through 834
      removed outlier: 6.749A  pdb=" N   PHE A 830 " --> pdb=" O   LEU A 896 " (cutoff:3.500A)

    195 hydrogen bonds defined for protein.
    549 hydrogen bond angles defined for protein.
NA hbond rejected because one of the atoms is absent
    Restraints generated for nucleic acids:
      22 hydrogen bonds
      44 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      13 stacking parallelities
  Total time for adding SS restraints: 1.08

  Time building geometry restraints manager: 0.58 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1875
        1.33 -     1.45: 1351
        1.45 -     1.57: 3867
        1.57 -     1.69: 67
        1.69 -     1.81: 52
  Bond restraints: 7212
  Sorted by residual:
  bond pdb=" CA  GLY A 434 "
       pdb=" C   GLY A 434 "
    ideal  model  delta    sigma   weight residual
    1.530  1.514  0.017 1.04e-02 9.25e+03 2.56e+00
  bond pdb=" CB  VAL A 928 "
       pdb=" CG2 VAL A 928 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.46e+00
  bond pdb=" N   GLY A 434 "
       pdb=" CA  GLY A 434 "
    ideal  model  delta    sigma   weight residual
    1.464  1.448  0.016 1.12e-02 7.97e+03 2.15e+00
  bond pdb=" C   TRP A 732 "
       pdb=" N   PRO A 733 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.23e-02 6.61e+03 2.12e+00
  bond pdb=" C   LEU A 533 "
       pdb=" N   PRO A 534 "
    ideal  model  delta    sigma   weight residual
    1.332  1.316  0.016 1.12e-02 7.97e+03 2.01e+00
  ... (remaining 7207 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 9282
        1.36 -     2.73: 514
        2.73 -     4.09: 91
        4.09 -     5.46: 23
        5.46 -     6.82: 7
  Bond angle restraints: 9917
  Sorted by residual:
  angle pdb=" C   THR A 866 "
        pdb=" N   LYS A 867 "
        pdb=" CA  LYS A 867 "
      ideal   model   delta    sigma   weight residual
     121.54  128.36   -6.82 1.91e+00 2.74e-01 1.27e+01
  angle pdb=" C3'   A B  12 "
        pdb=" O3'   A B  12 "
        pdb=" P     A B  13 "
      ideal   model   delta    sigma   weight residual
     120.20  125.55   -5.35 1.50e+00 4.44e-01 1.27e+01
  angle pdb=" C   GLY A 191 "
        pdb=" N   ARG A 192 "
        pdb=" CA  ARG A 192 "
      ideal   model   delta    sigma   weight residual
     121.54  128.21   -6.67 1.91e+00 2.74e-01 1.22e+01
  angle pdb=" N   LEU A 252 "
        pdb=" CA  LEU A 252 "
        pdb=" C   LEU A 252 "
      ideal   model   delta    sigma   weight residual
     114.31  110.02    4.29 1.29e+00 6.01e-01 1.11e+01
  angle pdb=" O3'   A B  12 "
        pdb=" C3'   A B  12 "
        pdb=" C2'   A B  12 "
      ideal   model   delta    sigma   weight residual
     109.50  114.18   -4.68 1.50e+00 4.44e-01 9.73e+00
  ... (remaining 9912 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.94: 4260
       35.94 -    71.89: 144
       71.89 -   107.83: 22
      107.83 -   143.77: 0
      143.77 -   179.72: 4
  Dihedral angle restraints: 4430
    sinusoidal: 2121
      harmonic: 2309
  Sorted by residual:
  dihedral pdb=" O4'   U B  19 "
           pdb=" C1'   U B  19 "
           pdb=" N1    U B  19 "
           pdb=" C2    U B  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   52.28  179.72     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" CA  GLU A 461 "
           pdb=" C   GLU A 461 "
           pdb=" N   LYS A 462 "
           pdb=" CA  LYS A 462 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.65   20.35     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" C4'   C D  20 "
           pdb=" C3'   C D  20 "
           pdb=" O3'   C D  20 "
           pdb=" P     A D  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.27  177.73     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 4427 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 875
       0.049 -    0.099: 223
       0.099 -    0.148: 38
       0.148 -    0.197: 2
       0.197 -    0.247: 1
  Chirality restraints: 1139
  Sorted by residual:
  chirality pdb=" CB  ILE A 927 "
            pdb=" CA  ILE A 927 "
            pdb=" CG1 ILE A 927 "
            pdb=" CG2 ILE A 927 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" C3'   A B  12 "
            pdb=" C4'   A B  12 "
            pdb=" O3'   A B  12 "
            pdb=" C2'   A B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.55   -0.19 2.00e-01 2.50e+01 9.41e-01
  chirality pdb=" CB  VAL A 678 "
            pdb=" CA  VAL A 678 "
            pdb=" CG1 VAL A 678 "
            pdb=" CG2 VAL A 678 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.15 2.00e-01 2.50e+01 6.00e-01
  ... (remaining 1136 not shown)

  Planarity restraints: 1150
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 732 "    0.014 2.00e-02 2.50e+03   1.19e-02 3.55e+00
        pdb=" CG  TRP A 732 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 732 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 732 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 732 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 732 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 732 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 732 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 732 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 732 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 300 "    0.139 9.50e-02 1.11e+02   6.28e-02 3.09e+00
        pdb=" NE  ARG A 300 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 300 "    0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 300 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 300 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 929 "    0.026 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO A 930 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 930 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 930 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1147 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 55
        2.51 -     3.11: 5007
        3.11 -     3.71: 10739
        3.71 -     4.30: 14223
        4.30 -     4.90: 23998
  Nonbonded interactions: 54022
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 709 "
            pdb="MG    MG A1001 "
     model   vdw
     1.915 2.170
  nonbonded pdb=" ND1 HIS A 935 "
            pdb="MG    MG A1001 "
     model   vdw
     2.071 2.250
  nonbonded pdb=" O2'   C D  20 "
            pdb=" OP1   A D  21 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" NH2 ARG A 940 "
            pdb=" OH  TYR A 944 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" NH2 ARG A 920 "
            pdb=" OP1   G B   3 "
     model   vdw
     2.202 3.120
  ... (remaining 54017 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:             0.500
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.070
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
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      :  0.004   0.052   7212  Z= 0.205
  Angle     :  0.736   6.819   9917  Z= 0.419
  Chirality :  0.043   0.247   1139
  Planarity :  0.005   0.063   1150
  Dihedral  : 18.242 179.716   2936
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.65 %
    Favored  : 89.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.38 (0.29), residues: 779
  helix: -0.54 (0.36), residues: 212
  sheet: -1.58 (0.50), residues: 118
  loop : -2.17 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 300 
 TYR   0.021   0.002   TYR A 638 
 PHE   0.025   0.002   PHE A 874 
 TRP   0.031   0.002   TRP A 732 
 HIS   0.005   0.001   HIS A 892 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 7212)
  covalent geometry    : angle       0.73631 ( 9917)
  hydrogen bonds       : bond        0.17742 (  217)
  hydrogen bonds       : angle       7.30096 (  593)

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

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

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 MET cc_start: 0.4031 (mmp) cc_final: 0.3448 (mmp)
REVERT: A  567 ASN cc_start: 0.7178 (t0) cc_final: 0.6943 (t0)
REVERT: A  912 ASN cc_start: 0.8469 (t0) cc_final: 0.8174 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0847
  time to fit residues: 14.4984
Evaluate side-chains
  81 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 602 GLN
A 609 HIS
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 846 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.121975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.089206 restraints weight = 16211.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.091992 restraints weight = 8206.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.093757 restraints weight = 5364.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.094810 restraints weight = 4145.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.095529 restraints weight = 3565.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7212  Z= 0.155
  Angle     :  0.648   7.933   9917  Z= 0.333
  Chirality :  0.043   0.188   1139
  Planarity :  0.005   0.038   1150
  Dihedral  : 17.804 178.582   1382
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.34 %
    Favored  : 91.66 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.74 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.10 (0.29), residues: 779
  helix:  0.15 (0.38), residues: 209
  sheet: -1.44 (0.47), residues: 131
  loop : -2.24 (0.27), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 361 
 TYR   0.016   0.002   TYR A 932 
 PHE   0.015   0.002   PHE A 874 
 TRP   0.018   0.002   TRP A 759 
 HIS   0.007   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7212)
  covalent geometry    : angle       0.64756 ( 9917)
  hydrogen bonds       : bond        0.03528 (  217)
  hydrogen bonds       : angle       5.45462 (  593)

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

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

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  345 GLN cc_start: 0.9612 (pt0) cc_final: 0.9097 (pp30)
REVERT: A  444 MET cc_start: 0.6245 (mmp) cc_final: 0.5521 (mmp)
REVERT: A  567 ASN cc_start: 0.7985 (t0) cc_final: 0.7771 (t0)
REVERT: A  575 GLU cc_start: 0.8759 (tp30) cc_final: 0.8471 (tp30)
REVERT: A  793 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8326 (t80)
  outliers start: 12
  outliers final: 10
  residues processed: 104
  average time/residue: 0.0746
  time to fit residues: 10.5873
Evaluate side-chains
  96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  479 GLU
Chi-restraints excluded: chain A residue  655 CYS
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  793 TYR
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain A residue  858 ILE
Chi-restraints excluded: chain A residue  869 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 26 optimal weight:   20.0000
   chunk 9 optimal weight:   20.0000
   chunk 54 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0670
   overall best weight:    2.1322

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 894 HIS ** 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 = 0.3891 r_free = 0.3891 target = 0.120570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.088422 restraints weight = 16147.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.091107 restraints weight = 8249.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.092860 restraints weight = 5445.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.093926 restraints weight = 4212.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.094451 restraints weight = 3617.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7212  Z= 0.160
  Angle     :  0.622   7.466   9917  Z= 0.324
  Chirality :  0.043   0.188   1139
  Planarity :  0.004   0.039   1150
  Dihedral  : 17.749 178.383   1382
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.35 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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: -1.97 (0.29), residues: 779
  helix:  0.27 (0.38), residues: 210
  sheet: -1.32 (0.47), residues: 132
  loop : -2.18 (0.27), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 361 
 TYR   0.027   0.002   TYR A 197 
 PHE   0.014   0.001   PHE A 874 
 TRP   0.012   0.002   TRP A 759 
 HIS   0.002   0.001   HIS A 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 7212)
  covalent geometry    : angle       0.62160 ( 9917)
  hydrogen bonds       : bond        0.03480 (  217)
  hydrogen bonds       : angle       5.32555 (  593)

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

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

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8061 (mm)
REVERT: A  213 TRP cc_start: 0.8257 (t60) cc_final: 0.8028 (t60)
REVERT: A  442 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8430 (pp)
REVERT: A  444 MET cc_start: 0.6310 (mmp) cc_final: 0.5704 (mmp)
REVERT: A  550 MET cc_start: 0.8110 (mmm) cc_final: 0.7664 (mmm)
REVERT: A  575 GLU cc_start: 0.8709 (tp30) cc_final: 0.8305 (tp30)
REVERT: A  793 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8366 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 98
  average time/residue: 0.0785
  time to fit residues: 10.4470
Evaluate side-chains
  88 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  208 GLU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  655 CYS
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  793 TYR
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain A residue  858 ILE
Chi-restraints excluded: chain A residue  869 CYS
Chi-restraints excluded: chain A residue  974 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 47 optimal weight:    8.9990
   chunk 12 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 81 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   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 158 ASN
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 850 ASN
** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 900 ASN
A 913 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.111117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.078329 restraints weight = 16651.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.080959 restraints weight = 8414.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.082570 restraints weight = 5484.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.083626 restraints weight = 4270.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.084143 restraints weight = 3663.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.3176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.073   7212  Z= 0.376
  Angle     :  0.814   9.536   9917  Z= 0.426
  Chirality :  0.050   0.208   1139
  Planarity :  0.006   0.057   1150
  Dihedral  : 18.040 176.437   1382
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.42 %
    Favored  : 88.58 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 16.96 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.28), residues: 779
  helix: -0.30 (0.35), residues: 216
  sheet: -1.05 (0.52), residues: 108
  loop : -2.58 (0.25), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 386 
 TYR   0.020   0.003   TYR A 738 
 PHE   0.034   0.003   PHE A 500 
 TRP   0.018   0.003   TRP A 732 
 HIS   0.004   0.002   HIS A 837 

Details of bonding type rmsd
  covalent geometry    : bond        0.00838 ( 7212)
  covalent geometry    : angle       0.81383 ( 9917)
  hydrogen bonds       : bond        0.04976 (  217)
  hydrogen bonds       : angle       5.85006 (  593)

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

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

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 65
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8443 (tp)
REVERT: A  183 ARG cc_start: 0.9243 (ptm160) cc_final: 0.8981 (ptm-80)
REVERT: A  337 LEU cc_start: 0.7885 (tp) cc_final: 0.7614 (tp)
REVERT: A  341 GLU cc_start: 0.8391 (pm20) cc_final: 0.8130 (pm20)
REVERT: A  444 MET cc_start: 0.6543 (mmp) cc_final: 0.6218 (mmp)
REVERT: A  550 MET cc_start: 0.8329 (mmm) cc_final: 0.7841 (mmm)
REVERT: A  575 GLU cc_start: 0.8863 (tp30) cc_final: 0.8475 (tp30)
REVERT: A  627 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8735 (mp)
REVERT: A  793 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8355 (t80)
REVERT: A  838 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.7733 (p90)
REVERT: A  920 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8671 (mtm180)
  outliers start: 28
  outliers final: 19
  residues processed: 88
  average time/residue: 0.0691
  time to fit residues: 8.4484
Evaluate side-chains
  85 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 61
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  186 LYS
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  479 GLU
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  655 CYS
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  793 TYR
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain A residue  830 PHE
Chi-restraints excluded: chain A residue  838 HIS
Chi-restraints excluded: chain A residue  858 ILE
Chi-restraints excluded: chain A residue  869 CYS
Chi-restraints excluded: chain A residue  915 CYS
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  974 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 24 optimal weight:    9.9990
   chunk 29 optimal weight:    0.0570
   chunk 36 optimal weight:    0.2980
   chunk 73 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
A 463 GLN
A 602 GLN
A 671 ASN
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 850 ASN
** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.121902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.089751 restraints weight = 16243.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.092612 restraints weight = 8175.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.094403 restraints weight = 5316.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.095376 restraints weight = 4111.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.096124 restraints weight = 3560.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7212  Z= 0.110
  Angle     :  0.597   7.600   9917  Z= 0.309
  Chirality :  0.042   0.185   1139
  Planarity :  0.004   0.039   1150
  Dihedral  : 17.727 178.893   1382
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 19.28 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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: -1.95 (0.29), residues: 779
  helix:  0.31 (0.38), residues: 210
  sheet: -1.22 (0.48), residues: 131
  loop : -2.23 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 599 
 TYR   0.013   0.001   TYR A 204 
 PHE   0.011   0.001   PHE A 291 
 TRP   0.020   0.002   TRP A 213 
 HIS   0.003   0.001   HIS A 892 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7212)
  covalent geometry    : angle       0.59708 ( 9917)
  hydrogen bonds       : bond        0.03158 (  217)
  hydrogen bonds       : angle       5.12485 (  593)

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

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

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  208 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8109 (tm-30)
REVERT: A  333 PHE cc_start: 0.8706 (m-80) cc_final: 0.8505 (m-10)
REVERT: A  345 GLN cc_start: 0.9560 (pt0) cc_final: 0.9207 (pp30)
REVERT: A  444 MET cc_start: 0.6326 (mmp) cc_final: 0.5996 (mmt)
REVERT: A  500 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7910 (t80)
REVERT: A  506 GLU cc_start: 0.8708 (tp30) cc_final: 0.8427 (tp30)
REVERT: A  550 MET cc_start: 0.8081 (mmm) cc_final: 0.7743 (mmm)
REVERT: A  575 GLU cc_start: 0.8566 (tp30) cc_final: 0.8259 (tp30)
REVERT: A  732 TRP cc_start: 0.6950 (t-100) cc_final: 0.6638 (t-100)
REVERT: A  771 MET cc_start: 0.7622 (mtm) cc_final: 0.7038 (mtm)
REVERT: A  793 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8284 (t80)
REVERT: A  896 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8739 (mm)
REVERT: A  932 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7785 (t80)
  outliers start: 22
  outliers final: 10
  residues processed: 101
  average time/residue: 0.0765
  time to fit residues: 10.4389
Evaluate side-chains
  88 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  208 GLU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  500 PHE
Chi-restraints excluded: chain A residue  655 CYS
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  793 TYR
Chi-restraints excluded: chain A residue  869 CYS
Chi-restraints excluded: chain A residue  884 ILE
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  932 TYR
Chi-restraints excluded: chain A residue  974 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 59 optimal weight:    8.9990
   chunk 63 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 73 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 26 optimal weight:   20.0000
   chunk 61 optimal weight:    0.9980
   chunk 67 optimal weight:    9.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 894 HIS ** 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 = 0.3813 r_free = 0.3813 target = 0.115181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.082382 restraints weight = 16636.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.084898 restraints weight = 8688.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.086538 restraints weight = 5847.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.087555 restraints weight = 4593.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.087973 restraints weight = 3971.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058   7212  Z= 0.298
  Angle     :  0.731   9.503   9917  Z= 0.379
  Chirality :  0.047   0.186   1139
  Planarity :  0.005   0.043   1150
  Dihedral  : 17.922 178.523   1382
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.27 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 20.29 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.33 (0.28), residues: 779
  helix:  0.02 (0.36), residues: 211
  sheet: -1.48 (0.47), residues: 126
  loop : -2.47 (0.26), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 599 
 TYR   0.016   0.002   TYR A 738 
 PHE   0.019   0.002   PHE A 874 
 TRP   0.017   0.002   TRP A 213 
 HIS   0.005   0.001   HIS A 881 

Details of bonding type rmsd
  covalent geometry    : bond        0.00663 ( 7212)
  covalent geometry    : angle       0.73056 ( 9917)
  hydrogen bonds       : bond        0.04279 (  217)
  hydrogen bonds       : angle       5.46161 (  593)

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

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

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 64
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  337 LEU cc_start: 0.7747 (tp) cc_final: 0.7421 (tp)
REVERT: A  341 GLU cc_start: 0.8394 (pm20) cc_final: 0.8185 (pm20)
REVERT: A  432 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6466 (mp10)
REVERT: A  500 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7932 (t80)
REVERT: A  550 MET cc_start: 0.8208 (mmm) cc_final: 0.7762 (mmm)
REVERT: A  575 GLU cc_start: 0.8663 (tp30) cc_final: 0.8358 (tp30)
REVERT: A  732 TRP cc_start: 0.7573 (t-100) cc_final: 0.7189 (t60)
REVERT: A  793 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8289 (t80)
REVERT: A  896 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8805 (mm)
REVERT: A  920 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8715 (mtm180)
REVERT: A  932 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8195 (t80)
  outliers start: 35
  outliers final: 19
  residues processed: 94
  average time/residue: 0.0789
  time to fit residues: 10.1080
Evaluate side-chains
  85 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 60
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  432 GLN
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  479 GLU
Chi-restraints excluded: chain A residue  500 PHE
Chi-restraints excluded: chain A residue  655 CYS
Chi-restraints excluded: chain A residue  671 ASN
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  793 TYR
Chi-restraints excluded: chain A residue  830 PHE
Chi-restraints excluded: chain A residue  858 ILE
Chi-restraints excluded: chain A residue  869 CYS
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  932 TYR
Chi-restraints excluded: chain A residue  974 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 80 optimal weight:   30.0000
   chunk 35 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 894 HIS ** 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 = 0.3879 r_free = 0.3879 target = 0.120949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.085471 restraints weight = 16396.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.088290 restraints weight = 8407.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.090109 restraints weight = 5591.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.091239 restraints weight = 4368.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.091809 restraints weight = 3775.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7212  Z= 0.150
  Angle     :  0.634   8.809   9917  Z= 0.326
  Chirality :  0.043   0.186   1139
  Planarity :  0.004   0.038   1150
  Dihedral  : 17.838 178.978   1382
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 22.32 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.29), residues: 779
  helix:  0.35 (0.38), residues: 210
  sheet: -1.59 (0.45), residues: 144
  loop : -2.30 (0.27), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 599 
 TYR   0.012   0.001   TYR A 204 
 PHE   0.014   0.001   PHE A 902 
 TRP   0.021   0.002   TRP A 213 
 HIS   0.002   0.001   HIS A 892 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7212)
  covalent geometry    : angle       0.63405 ( 9917)
  hydrogen bonds       : bond        0.03451 (  217)
  hydrogen bonds       : angle       5.16786 (  593)

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

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

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 ARG cc_start: 0.9341 (ptm160) cc_final: 0.8951 (ptm-80)
REVERT: A  211 PHE cc_start: 0.7451 (p90) cc_final: 0.7230 (p90)
REVERT: A  432 GLN cc_start: 0.6753 (OUTLIER) cc_final: 0.6267 (mp10)
REVERT: A  500 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8119 (t80)
REVERT: A  550 MET cc_start: 0.8252 (mmm) cc_final: 0.7817 (mmm)
REVERT: A  575 GLU cc_start: 0.8715 (tp30) cc_final: 0.8394 (tp30)
REVERT: A  732 TRP cc_start: 0.7465 (t-100) cc_final: 0.7008 (t60)
REVERT: A  793 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.8301 (t80)
REVERT: A  896 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8808 (mm)
REVERT: A  920 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8687 (mtm180)
REVERT: A  932 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7800 (t80)
  outliers start: 28
  outliers final: 16
  residues processed: 100
  average time/residue: 0.0758
  time to fit residues: 10.3422
Evaluate side-chains
  94 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  208 GLU
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  432 GLN
Chi-restraints excluded: chain A residue  479 GLU
Chi-restraints excluded: chain A residue  500 PHE
Chi-restraints excluded: chain A residue  653 SER
Chi-restraints excluded: chain A residue  655 CYS
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  780 ARG
Chi-restraints excluded: chain A residue  793 TYR
Chi-restraints excluded: chain A residue  830 PHE
Chi-restraints excluded: chain A residue  869 CYS
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  932 TYR
Chi-restraints excluded: chain A residue  974 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 79 optimal weight:    9.9990
   chunk 68 optimal weight:    0.3980
   chunk 20 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 78 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 894 HIS ** 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 = 0.3855 r_free = 0.3855 target = 0.117556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.085380 restraints weight = 16275.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.088042 restraints weight = 8178.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.089765 restraints weight = 5344.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.090778 restraints weight = 4122.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.091320 restraints weight = 3547.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7212  Z= 0.186
  Angle     :  0.656   9.106   9917  Z= 0.338
  Chirality :  0.044   0.185   1139
  Planarity :  0.004   0.039   1150
  Dihedral  : 17.840 179.474   1382
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 22.46 %
    Favored  : 73.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.29), residues: 779
  helix:  0.18 (0.37), residues: 218
  sheet: -1.65 (0.45), residues: 142
  loop : -2.37 (0.27), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 599 
 TYR   0.011   0.002   TYR A 932 
 PHE   0.013   0.002   PHE A 874 
 TRP   0.021   0.002   TRP A 213 
 HIS   0.002   0.001   HIS A 892 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 7212)
  covalent geometry    : angle       0.65633 ( 9917)
  hydrogen bonds       : bond        0.03656 (  217)
  hydrogen bonds       : angle       5.15603 (  593)

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

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

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 72
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 PHE cc_start: 0.7381 (p90) cc_final: 0.7168 (p90)
REVERT: A  432 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6578 (mp10)
REVERT: A  500 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7965 (t80)
REVERT: A  550 MET cc_start: 0.8239 (mmm) cc_final: 0.7770 (mmm)
REVERT: A  575 GLU cc_start: 0.8628 (tp30) cc_final: 0.8384 (tp30)
REVERT: A  732 TRP cc_start: 0.7425 (t-100) cc_final: 0.7059 (t60)
REVERT: A  793 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.8273 (t80)
REVERT: A  896 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8777 (mm)
REVERT: A  920 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8690 (mtm180)
REVERT: A  932 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.7961 (t80)
  outliers start: 30
  outliers final: 18
  residues processed: 98
  average time/residue: 0.0807
  time to fit residues: 10.5003
Evaluate side-chains
  94 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  208 GLU
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  432 GLN
Chi-restraints excluded: chain A residue  479 GLU
Chi-restraints excluded: chain A residue  500 PHE
Chi-restraints excluded: chain A residue  653 SER
Chi-restraints excluded: chain A residue  655 CYS
Chi-restraints excluded: chain A residue  671 ASN
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  780 ARG
Chi-restraints excluded: chain A residue  793 TYR
Chi-restraints excluded: chain A residue  830 PHE
Chi-restraints excluded: chain A residue  869 CYS
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  932 TYR
Chi-restraints excluded: chain A residue  974 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 894 HIS ** 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 = 0.3869 r_free = 0.3869 target = 0.118543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.086384 restraints weight = 16114.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.089090 restraints weight = 8091.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.090814 restraints weight = 5254.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.091905 restraints weight = 4044.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.092446 restraints weight = 3454.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7212  Z= 0.154
  Angle     :  0.644   9.146   9917  Z= 0.329
  Chirality :  0.043   0.185   1139
  Planarity :  0.004   0.039   1150
  Dihedral  : 17.818 178.808   1382
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 23.48 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.29), residues: 779
  helix:  0.45 (0.38), residues: 212
  sheet: -1.69 (0.43), residues: 155
  loop : -2.31 (0.27), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 599 
 TYR   0.010   0.001   TYR A 204 
 PHE   0.010   0.001   PHE A 148 
 TRP   0.023   0.002   TRP A 213 
 HIS   0.002   0.001   HIS A 892 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7212)
  covalent geometry    : angle       0.64354 ( 9917)
  hydrogen bonds       : bond        0.03498 (  217)
  hydrogen bonds       : angle       5.06189 (  593)

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

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

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 72
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  183 ARG cc_start: 0.9262 (ptm160) cc_final: 0.8934 (ptm-80)
REVERT: A  432 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6512 (mp10)
REVERT: A  500 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7857 (t80)
REVERT: A  550 MET cc_start: 0.8196 (mmm) cc_final: 0.7742 (mmm)
REVERT: A  575 GLU cc_start: 0.8587 (tp30) cc_final: 0.8370 (tp30)
REVERT: A  732 TRP cc_start: 0.7298 (t-100) cc_final: 0.6926 (t60)
REVERT: A  793 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.8293 (t80)
REVERT: A  896 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8733 (mm)
REVERT: A  920 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8727 (mtm180)
REVERT: A  932 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7867 (t80)
  outliers start: 28
  outliers final: 19
  residues processed: 97
  average time/residue: 0.0768
  time to fit residues: 10.3638
Evaluate side-chains
  97 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 72
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  208 GLU
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  432 GLN
Chi-restraints excluded: chain A residue  479 GLU
Chi-restraints excluded: chain A residue  500 PHE
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain A residue  653 SER
Chi-restraints excluded: chain A residue  655 CYS
Chi-restraints excluded: chain A residue  671 ASN
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  780 ARG
Chi-restraints excluded: chain A residue  793 TYR
Chi-restraints excluded: chain A residue  830 PHE
Chi-restraints excluded: chain A residue  869 CYS
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  932 TYR
Chi-restraints excluded: chain A residue  974 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 26 optimal weight:   30.0000
   chunk 52 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 894 HIS ** 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 = 0.3821 r_free = 0.3821 target = 0.115499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.083236 restraints weight = 16137.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.085815 restraints weight = 8238.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.087480 restraints weight = 5412.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.088480 restraints weight = 4213.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.089044 restraints weight = 3634.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   7212  Z= 0.267
  Angle     :  0.729   9.726   9917  Z= 0.376
  Chirality :  0.046   0.185   1139
  Planarity :  0.005   0.041   1150
  Dihedral  : 17.919 179.915   1382
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.65 %
    Favored  : 89.35 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 23.48 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.29), residues: 779
  helix:  0.26 (0.37), residues: 215
  sheet: -1.72 (0.45), residues: 142
  loop : -2.46 (0.26), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 276 
 TYR   0.014   0.002   TYR A 793 
 PHE   0.018   0.002   PHE A 874 
 TRP   0.026   0.002   TRP A 213 
 HIS   0.003   0.001   HIS A 881 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 7212)
  covalent geometry    : angle       0.72938 ( 9917)
  hydrogen bonds       : bond        0.04161 (  217)
  hydrogen bonds       : angle       5.27553 (  593)

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

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

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1558 Ramachandran restraints generated.
    779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 68
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  238 LYS cc_start: 0.8983 (mtmm) cc_final: 0.8707 (pttm)
REVERT: A  432 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6590 (mp10)
REVERT: A  500 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7867 (t80)
REVERT: A  550 MET cc_start: 0.8291 (mmm) cc_final: 0.7817 (mmm)
REVERT: A  575 GLU cc_start: 0.8639 (tp30) cc_final: 0.8416 (tp30)
REVERT: A  732 TRP cc_start: 0.7608 (t-100) cc_final: 0.7074 (t-100)
REVERT: A  793 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8287 (t80)
REVERT: A  896 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8764 (mm)
REVERT: A  920 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8777 (mtm180)
REVERT: A  932 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8120 (t80)
  outliers start: 30
  outliers final: 22
  residues processed: 94
  average time/residue: 0.0791
  time to fit residues: 10.0100
Evaluate side-chains
  96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  208 GLU
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  318 THR
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  432 GLN
Chi-restraints excluded: chain A residue  479 GLU
Chi-restraints excluded: chain A residue  500 PHE
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain A residue  653 SER
Chi-restraints excluded: chain A residue  655 CYS
Chi-restraints excluded: chain A residue  671 ASN
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  780 ARG
Chi-restraints excluded: chain A residue  793 TYR
Chi-restraints excluded: chain A residue  830 PHE
Chi-restraints excluded: chain A residue  858 ILE
Chi-restraints excluded: chain A residue  869 CYS
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  932 TYR
Chi-restraints excluded: chain A residue  974 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 72 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 80 optimal weight:   30.0000
   chunk 26 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 671 ASN
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 894 HIS ** 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 = 0.3857 r_free = 0.3857 target = 0.117836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.085744 restraints weight = 16055.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.088395 restraints weight = 8068.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.090133 restraints weight = 5278.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.091114 restraints weight = 4068.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.091744 restraints weight = 3504.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7212  Z= 0.164
  Angle     :  0.658   9.416   9917  Z= 0.338
  Chirality :  0.044   0.185   1139
  Planarity :  0.004   0.039   1150
  Dihedral  : 17.846 178.434   1382
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 23.77 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.29), residues: 779
  helix:  0.49 (0.38), residues: 212
  sheet: -1.63 (0.45), residues: 142
  loop : -2.38 (0.26), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 599 
 TYR   0.010   0.001   TYR A 204 
 PHE   0.012   0.002   PHE A 874 
 TRP   0.025   0.002   TRP A 213 
 HIS   0.002   0.001   HIS A 892 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 7212)
  covalent geometry    : angle       0.65760 ( 9917)
  hydrogen bonds       : bond        0.03565 (  217)
  hydrogen bonds       : angle       5.08940 (  593)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1128.16 seconds
wall clock time: 20 minutes 14.27 seconds (1214.27 seconds total)