Starting phenix.real_space_refine
on Tue Feb 13 17:19:26 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gua_34271/02_2024/8gua_34271_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gua_34271/02_2024/8gua_34271.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gua_34271/02_2024/8gua_34271.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gua_34271/02_2024/8gua_34271.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gua_34271/02_2024/8gua_34271_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gua_34271/02_2024/8gua_34271_updated.pdb"
  }
  resolution = 2.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.055
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    4481      2.51       5
     N    1204      2.21       5
     O    1267      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  127": "OE1" <-> "OE2"
    Residue "A GLU  563": "OE1" <-> "OE2"
    Residue "A PHE  937": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1034": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 7017
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 856, 7017
          Unusual residues: {'1LT': 1}
          Classifications: {'peptide': 855, 'undetermined': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 814, None: 1}
            Not linked:
              pdbres="GLY A1050 "
              pdbres="1LT A1101 "
          Chain breaks: 7
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   ILE A 932 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CD1 ILE A 932 " occ=0.50
    residue:
      pdb=" N   ASP A 933 " occ=0.50
      ... (6 atoms not shown)
      pdb=" OD2 ASP A 933 " occ=0.50
    residue:
      pdb=" N   PHE A 934 " occ=0.50
      ... (9 atoms not shown)
      pdb=" CZ  PHE A 934 " occ=0.50
    residue:
      pdb=" N   GLY A 935 " occ=0.50
      ... (2 atoms not shown)
      pdb=" O   GLY A 935 " occ=0.50
  Time building chain proxies: 4.01, per 1000 atoms: 0.57
  Number of scatterers: 7017
  At special positions: 0
  Unit cell: (79.254, 95.319, 103.887, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      62     16.00
     F       3      9.00
     O    1267      8.00
     N    1204      7.00
     C    4481      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.43
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1638

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      39 helices and 5 sheets defined
      43.9% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 108 through 121
      removed outlier: 3.792A  pdb=" N   ARG A 115 " --> pdb=" O   LYS A 111 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLU A 116 " --> pdb=" O   ILE A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 129
      No H-bonds generated for 'chain 'A' and resid 126 through 129'
    Processing helix  chain 'A' and resid 134 through 140
    Processing helix  chain 'A' and resid 145 through 154
    Processing helix  chain 'A' and resid 160 through 166
    Processing helix  chain 'A' and resid 179 through 184
    Processing helix  chain 'A' and resid 217 through 228
      removed outlier: 4.110A  pdb=" N   ILE A 221 " --> pdb=" O   PRO A 217 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ALA A 222 " --> pdb=" O   GLU A 218 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLU A 223 " --> pdb=" O   GLN A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 279
    Processing helix  chain 'A' and resid 290 through 296
      removed outlier: 3.630A  pdb=" N   GLN A 296 " --> pdb=" O   SER A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 308
      No H-bonds generated for 'chain 'A' and resid 306 through 308'
    Processing helix  chain 'A' and resid 393 through 395
      No H-bonds generated for 'chain 'A' and resid 393 through 395'
    Processing helix  chain 'A' and resid 489 through 499
      removed outlier: 3.560A  pdb=" N   SER A 499 " --> pdb=" O   HIS A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 535
      removed outlier: 3.608A  pdb=" N   LYS A 532 " --> pdb=" O   LYS A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 553
    Processing helix  chain 'A' and resid 555 through 558
      No H-bonds generated for 'chain 'A' and resid 555 through 558'
    Processing helix  chain 'A' and resid 562 through 571
      Proline residue:  A 566  - end of helix
      removed outlier: 3.743A  pdb=" N   LEU A 569 " --> pdb=" O   PRO A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 588
      removed outlier: 3.515A  pdb=" N   CYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU A 586 " --> pdb=" O   GLN A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 602
      removed outlier: 4.146A  pdb=" N   GLU A 600 " --> pdb=" O   GLU A 596 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   LEU A 601 " --> pdb=" O   GLN A 597 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   LEU A 602 " --> pdb=" O   ALA A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 622
      removed outlier: 3.501A  pdb=" N   ALA A 615 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   VAL A 616 " --> pdb=" O   ARG A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 637
      removed outlier: 4.942A  pdb=" N   ILE A 633 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
      removed outlier: 5.484A  pdb=" N   GLN A 634 " --> pdb=" O   GLN A 630 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLN A 637 " --> pdb=" O   ILE A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 657
    Processing helix  chain 'A' and resid 661 through 674
    Processing helix  chain 'A' and resid 681 through 692
    Processing helix  chain 'A' and resid 696 through 721
      removed outlier: 3.521A  pdb=" N   LYS A 700 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU A 707 " --> pdb=" O   ARG A 704 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU A 710 " --> pdb=" O   GLU A 707 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ILE A 713 " --> pdb=" O   GLU A 710 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASN A 714 " --> pdb=" O   LYS A 711 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR A 716 " --> pdb=" O   ILE A 713 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE A 718 " --> pdb=" O   LEU A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 739
    Processing helix  chain 'A' and resid 742 through 748
      removed outlier: 3.696A  pdb=" N   ALA A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 792
      No H-bonds generated for 'chain 'A' and resid 790 through 792'
    Processing helix  chain 'A' and resid 808 through 827
    Processing helix  chain 'A' and resid 857 through 860
      No H-bonds generated for 'chain 'A' and resid 857 through 860'
    Processing helix  chain 'A' and resid 876 through 883
      removed outlier: 3.503A  pdb=" N   LEU A 881 " --> pdb=" O   LEU A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 910
      removed outlier: 3.735A  pdb=" N   PHE A 897 " --> pdb=" O   ALA A 893 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG A 899 " --> pdb=" O   ASP A 895 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY A 903 " --> pdb=" O   ARG A 899 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   TYR A 904 " --> pdb=" O   SER A 900 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 918 through 920
      No H-bonds generated for 'chain 'A' and resid 918 through 920'
    Processing helix  chain 'A' and resid 959 through 964
      removed outlier: 3.939A  pdb=" N   VAL A 963 " --> pdb=" O   ASP A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 1000
      removed outlier: 3.745A  pdb=" N   ARG A 979 " --> pdb=" O   ARG A 975 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   CYS A 984 " --> pdb=" O   PHE A 980 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR A 988 " --> pdb=" O   CYS A 984 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   LEU A 989 " --> pdb=" O   TYR A 985 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   ALA A 990 " --> pdb=" O   LYS A 986 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE A 991 " --> pdb=" O   ALA A 987 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   ASN A 996 " --> pdb=" O   ARG A 992 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   LEU A 997 " --> pdb=" O   GLN A 993 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1008
    Processing helix  chain 'A' and resid 1011 through 1013
      No H-bonds generated for 'chain 'A' and resid 1011 through 1013'
    Processing helix  chain 'A' and resid 1016 through 1018
      No H-bonds generated for 'chain 'A' and resid 1016 through 1018'
    Processing helix  chain 'A' and resid 1020 through 1026
    Processing helix  chain 'A' and resid 1032 through 1046
      removed outlier: 3.628A  pdb=" N   LEU A1036 " --> pdb=" O   GLU A1032 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   GLU A1037 " --> pdb=" O   GLN A1033 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   TYR A1038 " --> pdb=" O   GLU A1034 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   PHE A1039 " --> pdb=" O   ALA A1035 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASP A1045 " --> pdb=" O   LYS A1041 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA A1046 " --> pdb=" O   GLN A1042 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 205 through 212
      removed outlier: 3.555A  pdb=" N   ILE A 211 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   TRP A 195 " --> pdb=" O   PRO A 283 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   LEU A 285 " --> pdb=" O   TRP A 195 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 385 through 388
      removed outlier: 7.147A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ALA A 341 " --> pdb=" O   CYS A 472 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   CYS A 472 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 354 through 361
      removed outlier: 5.856A  pdb=" N   SER A 408 " --> pdb=" O   PRO A 421 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'A' and resid 779 through 784
      removed outlier: 3.514A  pdb=" N   GLY A 846 " --> pdb=" O   LYS A 802 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL A 845 " --> pdb=" O   GLY A 842 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   LEU A 847 " --> pdb=" O   SER A 840 " (cutoff:3.500A)
      removed outlier: 5.814A  pdb=" N   SER A 840 " --> pdb=" O   LEU A 847 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   GLU A 849 " --> pdb=" O   CYS A 838 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   CYS A 838 " --> pdb=" O   GLU A 849 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 854 through 856
      removed outlier: 3.528A  pdb=" N   HIS A 855 " --> pdb=" O   VAL A 923 " (cutoff:3.500A)

    227 hydrogen bonds defined for protein.
    588 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.43

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1160
        1.30 -     1.43: 1820
        1.43 -     1.56: 4092
        1.56 -     1.68: 7
        1.68 -     1.81: 94
  Bond restraints: 7173
  Sorted by residual:
  bond pdb=" C9  1LT A1101 "
       pdb=" S   1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.738  1.530  0.208 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" C2  1LT A1101 "
       pdb=" S   1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.734  1.533  0.201 2.00e-02 2.50e+03 1.01e+02
  bond pdb=" N   1LT A1101 "
       pdb=" C1  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.368  1.568 -0.200 2.00e-02 2.50e+03 1.00e+02
  bond pdb=" C5  1LT A1101 "
       pdb=" C6  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.525  1.350  0.175 2.00e-02 2.50e+03 7.62e+01
  bond pdb=" N   1LT A1101 "
       pdb=" C2  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.291  1.415 -0.124 2.00e-02 2.50e+03 3.84e+01
  ... (remaining 7168 not shown)

  Histogram of bond angle deviations from ideal:
       97.98 -   105.92: 170
      105.92 -   113.85: 4051
      113.85 -   121.78: 3927
      121.78 -   129.71: 1489
      129.71 -   137.64: 59
  Bond angle restraints: 9696
  Sorted by residual:
  angle pdb=" N1  1LT A1101 "
        pdb=" C2  1LT A1101 "
        pdb=" S   1LT A1101 "
      ideal   model   delta    sigma   weight residual
     118.47  137.64  -19.17 3.00e+00 1.11e-01 4.09e+01
  angle pdb=" C   TRP A 446 "
        pdb=" N   PRO A 447 "
        pdb=" CA  PRO A 447 "
      ideal   model   delta    sigma   weight residual
     120.03  113.74    6.29 9.90e-01 1.02e+00 4.04e+01
  angle pdb=" C2  1LT A1101 "
        pdb=" S   1LT A1101 "
        pdb=" C9  1LT A1101 "
      ideal   model   delta    sigma   weight residual
      88.90  107.66  -18.76 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" N   1LT A1101 "
        pdb=" C2  1LT A1101 "
        pdb=" N1  1LT A1101 "
      ideal   model   delta    sigma   weight residual
     126.74  114.29   12.45 3.00e+00 1.11e-01 1.72e+01
  angle pdb=" N   PRO A 449 "
        pdb=" CA  PRO A 449 "
        pdb=" C   PRO A 449 "
      ideal   model   delta    sigma   weight residual
     112.47  120.27   -7.80 2.06e+00 2.36e-01 1.43e+01
  ... (remaining 9691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 3868
       17.85 -    35.69: 408
       35.69 -    53.54: 71
       53.54 -    71.39: 15
       71.39 -    89.24: 7
  Dihedral angle restraints: 4369
    sinusoidal: 1851
      harmonic: 2518
  Sorted by residual:
  dihedral pdb=" C   PHE A 937 "
           pdb=" N   PHE A 937 "
           pdb=" CA  PHE A 937 "
           pdb=" CB  PHE A 937 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.55    8.95     0      2.50e+00 1.60e-01 1.28e+01
  dihedral pdb=" N   PHE A 937 "
           pdb=" C   PHE A 937 "
           pdb=" CA  PHE A 937 "
           pdb=" CB  PHE A 937 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.99   -8.19     0      2.50e+00 1.60e-01 1.07e+01
  dihedral pdb=" CA  PRO A 539 "
           pdb=" C   PRO A 539 "
           pdb=" N   LEU A 540 "
           pdb=" CA  LEU A 540 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.70   16.30     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 4366 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 966
       0.069 -    0.139: 82
       0.139 -    0.208: 2
       0.208 -    0.278: 2
       0.278 -    0.347: 2
  Chirality restraints: 1054
  Sorted by residual:
  chirality pdb=" CA  PRO A 449 "
            pdb=" N   PRO A 449 "
            pdb=" C   PRO A 449 "
            pdb=" CB  PRO A 449 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.02e+00
  chirality pdb=" CA  PHE A 937 "
            pdb=" N   PHE A 937 "
            pdb=" C   PHE A 937 "
            pdb=" CB  PHE A 937 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" CA  LEU A 938 "
            pdb=" N   LEU A 938 "
            pdb=" C   LEU A 938 "
            pdb=" CB  LEU A 938 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 1051 not shown)

  Planarity restraints: 1238
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 448 "   -0.069 5.00e-02 4.00e+02   1.03e-01 1.70e+01
        pdb=" N   PRO A 449 "    0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO A 449 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO A 449 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 159 "    0.017 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   PRO A 159 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   PRO A 159 "    0.025 2.00e-02 2.50e+03
        pdb=" N   HIS A 160 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 858 "   -0.011 2.00e-02 2.50e+03   2.15e-02 4.60e+00
        pdb=" C   MET A 858 "    0.037 2.00e-02 2.50e+03
        pdb=" O   MET A 858 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLN A 859 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1235 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1094
        2.76 -     3.29: 6918
        3.29 -     3.83: 11653
        3.83 -     4.36: 14615
        4.36 -     4.90: 23821
  Nonbonded interactions: 58101
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 900 "
            pdb=" O   LEU A 929 "
     model   vdw
     2.224 2.440
  nonbonded pdb=" OH  TYR A 584 "
            pdb=" OD1 ASP A 608 "
     model   vdw
     2.235 2.440
  nonbonded pdb=" O   GLU A 722 "
            pdb=" NE2 GLN A 731 "
     model   vdw
     2.245 2.520
  nonbonded pdb=" NH1 ARG A 808 "
            pdb=" O   SER A1008 "
     model   vdw
     2.248 2.520
  nonbonded pdb=" NE2 GLN A 825 "
            pdb=" O   LEU A 831 "
     model   vdw
     2.251 2.520
  ... (remaining 58096 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.190
  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:          3.980
  Check model and map are aligned:         0.100
  Set scattering table:                    0.080
  Process input model:                     21.530
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  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:11.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5968
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.208   7173  Z= 0.485
  Angle     :  0.695  19.175   9696  Z= 0.345
  Chirality :  0.044   0.347   1054
  Planarity :  0.005   0.103   1238
  Dihedral  : 15.036  89.236   2731
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.81 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.77 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.29), residues: 839
  helix: -0.84 (0.27), residues: 363
  sheet:  0.24 (0.51), residues: 98
  loop : -0.20 (0.35), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 783 
 HIS   0.003   0.001   HIS A 160 
 PHE   0.012   0.001   PHE A 960 
 TYR   0.024   0.001   TYR A 392 
 ARG   0.005   0.000   ARG A 382 

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.803 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 1.2115
  time to fit residues: 132.0135
Evaluate side-chains
  78 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0270
   chunk 43 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
A 643 GLN
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6016
moved from start:          0.1280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   7173  Z= 0.219
  Angle     :  0.587   6.243   9696  Z= 0.303
  Chirality :  0.042   0.224   1054
  Planarity :  0.006   0.100   1238
  Dihedral  :  5.272  35.062    943
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.81 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.48 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.28), residues: 839
  helix: -0.67 (0.25), residues: 381
  sheet:  0.41 (0.49), residues: 99
  loop : -0.38 (0.35), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A 936 
 PHE   0.012   0.001   PHE A 937 
 TYR   0.019   0.002   TYR A 392 
 ARG   0.007   0.000   ARG A 382 

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.706 
Fit side-chains
REVERT: A  547 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.6111 (tt0)
REVERT: A  594 LYS cc_start: 0.6811 (mmtm) cc_final: 0.6248 (mmpt)
REVERT: A  599 MET cc_start: 0.6437 (mtp) cc_final: 0.6066 (mtm)
REVERT: A  682 GLN cc_start: 0.6651 (mp-120) cc_final: 0.5778 (mt0)
REVERT: A  983 MET cc_start: 0.5421 (ttm) cc_final: 0.4350 (ptt)
  outliers start: 10
  outliers final: 3
  residues processed: 97
  average time/residue: 1.1214
  time to fit residues: 115.5074
Evaluate side-chains
  85 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  553 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 42 optimal weight:    0.0470
   chunk 23 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 52 optimal weight:    0.1980
   chunk 21 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 76 optimal weight:    0.1980
   chunk 26 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.3478

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

Flipped N/Q/H residues before XYZ refinement:
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 873 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5972
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   7173  Z= 0.159
  Angle     :  0.521   6.296   9696  Z= 0.266
  Chirality :  0.041   0.221   1054
  Planarity :  0.005   0.096   1238
  Dihedral  :  4.854  34.227    943
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.69 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.07 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.29), residues: 839
  helix: -0.33 (0.26), residues: 377
  sheet:  0.50 (0.49), residues: 98
  loop : -0.22 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 665 
 PHE   0.011   0.001   PHE A 794 
 TYR   0.015   0.001   TYR A 392 
 ARG   0.008   0.000   ARG A 382 

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A  599 MET cc_start: 0.6454 (mtp) cc_final: 0.6113 (mtm)
REVERT: A  682 GLN cc_start: 0.6664 (mp-120) cc_final: 0.5767 (mt0)
REVERT: A  820 MET cc_start: 0.7041 (mtt) cc_final: 0.6740 (mtt)
REVERT: A  979 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5245 (mtt-85)
REVERT: A  983 MET cc_start: 0.5377 (ttm) cc_final: 0.4307 (ptt)
REVERT: A 1039 PHE cc_start: 0.4664 (t80) cc_final: 0.4462 (t80)
  outliers start: 14
  outliers final: 3
  residues processed: 99
  average time/residue: 1.0179
  time to fit residues: 107.7624
Evaluate side-chains
  88 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  810 ASP
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 76 optimal weight:    0.0010
   chunk 58 optimal weight:    0.1980
   chunk 40 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0870
   chunk 73 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0270
   overall best weight:    0.2022

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

Flipped N/Q/H residues before XYZ refinement:
A 637 GLN
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 873 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5939
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.064   7173  Z= 0.143
  Angle     :  0.504   7.066   9696  Z= 0.255
  Chirality :  0.040   0.218   1054
  Planarity :  0.005   0.092   1238
  Dihedral  :  4.702  34.415    943
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.46 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.96 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.29), residues: 839
  helix: -0.04 (0.26), residues: 378
  sheet:  0.54 (0.50), residues: 96
  loop : -0.08 (0.35), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 669 
 HIS   0.003   0.000   HIS A 665 
 PHE   0.015   0.001   PHE A 960 
 TYR   0.014   0.001   TYR A 432 
 ARG   0.009   0.000   ARG A 382 

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A  264 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7114 (tttm)
REVERT: A  599 MET cc_start: 0.6430 (mtp) cc_final: 0.6070 (mtm)
REVERT: A  682 GLN cc_start: 0.6707 (mp-120) cc_final: 0.5788 (mt0)
REVERT: A  979 ARG cc_start: 0.6275 (OUTLIER) cc_final: 0.5301 (mtt-85)
REVERT: A  983 MET cc_start: 0.5262 (ttm) cc_final: 0.4310 (ptt)
  outliers start: 21
  outliers final: 5
  residues processed: 106
  average time/residue: 0.9889
  time to fit residues: 112.0798
Evaluate side-chains
  94 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  873 ASN
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 637 GLN
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 873 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6107
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   7173  Z= 0.301
  Angle     :  0.648   6.977   9696  Z= 0.329
  Chirality :  0.045   0.218   1054
  Planarity :  0.006   0.091   1238
  Dihedral  :  5.318  35.873    943
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.77 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 17.09 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.29), residues: 839
  helix: -0.32 (0.26), residues: 373
  sheet:  0.14 (0.48), residues: 96
  loop : -0.28 (0.35), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 386 
 HIS   0.005   0.001   HIS A 875 
 PHE   0.023   0.002   PHE A 666 
 TYR   0.034   0.002   TYR A 904 
 ARG   0.006   0.001   ARG A 382 

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A  264 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7127 (tttm)
REVERT: A  441 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6907 (ttp)
REVERT: A  594 LYS cc_start: 0.6906 (mmtm) cc_final: 0.6395 (mmpt)
REVERT: A  599 MET cc_start: 0.6630 (mtp) cc_final: 0.6093 (mtm)
REVERT: A  682 GLN cc_start: 0.6752 (mp-120) cc_final: 0.5805 (mt0)
REVERT: A  926 ASP cc_start: 0.4451 (OUTLIER) cc_final: 0.4191 (t70)
REVERT: A  936 HIS cc_start: 0.5555 (OUTLIER) cc_final: 0.4839 (p-80)
REVERT: A  979 ARG cc_start: 0.6261 (OUTLIER) cc_final: 0.5204 (mtt-85)
  outliers start: 26
  outliers final: 8
  residues processed: 108
  average time/residue: 1.0930
  time to fit residues: 125.5683
Evaluate side-chains
  104 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  441 MET
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  810 ASP
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain A residue  926 ASP
Chi-restraints excluded: chain A residue  936 HIS
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 73 optimal weight:    0.2980
   chunk 16 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 637 GLN
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6062
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7173  Z= 0.208
  Angle     :  0.575   8.394   9696  Z= 0.290
  Chirality :  0.042   0.218   1054
  Planarity :  0.005   0.089   1238
  Dihedral  :  5.118  34.443    943
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.29 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.49 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.29), residues: 839
  helix: -0.31 (0.26), residues: 381
  sheet:  0.07 (0.48), residues: 96
  loop : -0.29 (0.35), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A 665 
 PHE   0.015   0.002   PHE A 960 
 TYR   0.025   0.002   TYR A 904 
 ARG   0.008   0.000   ARG A 777 

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.783 
Fit side-chains
REVERT: A  264 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.7135 (tttm)
REVERT: A  267 LEU cc_start: 0.6932 (tp) cc_final: 0.6697 (tp)
REVERT: A  278 MET cc_start: 0.4345 (mmp) cc_final: 0.3298 (ttm)
REVERT: A  441 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.6906 (ttp)
REVERT: A  594 LYS cc_start: 0.6906 (mmtm) cc_final: 0.6385 (mmpt)
REVERT: A  599 MET cc_start: 0.6517 (mtp) cc_final: 0.6293 (mtp)
REVERT: A  682 GLN cc_start: 0.6798 (mp-120) cc_final: 0.5830 (mt0)
REVERT: A  833 MET cc_start: 0.4976 (OUTLIER) cc_final: 0.4387 (mtp)
REVERT: A  979 ARG cc_start: 0.6262 (OUTLIER) cc_final: 0.5216 (mtt-85)
REVERT: A  983 MET cc_start: 0.5452 (ttm) cc_final: 0.4411 (ptt)
REVERT: A 1004 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.5659 (mmm)
  outliers start: 25
  outliers final: 7
  residues processed: 105
  average time/residue: 0.9614
  time to fit residues: 108.1976
Evaluate side-chains
  98 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  441 MET
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  810 ASP
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain A residue  979 ARG
Chi-restraints excluded: chain A residue 1004 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0670
   chunk 69 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0670
   chunk 51 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0870
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.4034

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 637 GLN
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 917 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6017
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7173  Z= 0.169
  Angle     :  0.537   7.131   9696  Z= 0.271
  Chirality :  0.041   0.217   1054
  Planarity :  0.005   0.088   1238
  Dihedral  :  4.914  33.868    943
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.81 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 19.90 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.29), residues: 839
  helix: -0.10 (0.26), residues: 381
  sheet:  0.40 (0.51), residues: 89
  loop : -0.18 (0.35), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 665 
 PHE   0.014   0.002   PHE A 909 
 TYR   0.024   0.001   TYR A 904 
 ARG   0.011   0.000   ARG A 382 

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.857 
Fit side-chains
REVERT: A  267 LEU cc_start: 0.6788 (tp) cc_final: 0.6583 (tp)
REVERT: A  278 MET cc_start: 0.4371 (mmp) cc_final: 0.3281 (ttm)
REVERT: A  441 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.6901 (ttp)
REVERT: A  594 LYS cc_start: 0.6884 (mmtm) cc_final: 0.6388 (mmpt)
REVERT: A  682 GLN cc_start: 0.6805 (mp-120) cc_final: 0.5785 (mt0)
REVERT: A  833 MET cc_start: 0.4628 (OUTLIER) cc_final: 0.4219 (mtp)
REVERT: A  926 ASP cc_start: 0.4596 (OUTLIER) cc_final: 0.4327 (t70)
REVERT: A  979 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5246 (mtt-85)
REVERT: A  983 MET cc_start: 0.5320 (ttm) cc_final: 0.4389 (ptt)
  outliers start: 19
  outliers final: 8
  residues processed: 107
  average time/residue: 1.0306
  time to fit residues: 117.7077
Evaluate side-chains
  101 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  441 MET
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  810 ASP
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain A residue  926 ASP
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.2980
   chunk 64 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   chunk 78 optimal weight:    0.4980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 637 GLN
** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6031
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   7173  Z= 0.191
  Angle     :  0.555   6.649   9696  Z= 0.279
  Chirality :  0.042   0.229   1054
  Planarity :  0.005   0.083   1238
  Dihedral  :  4.954  34.315    943
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.17 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 19.52 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.29), residues: 839
  helix: -0.10 (0.26), residues: 385
  sheet:  0.47 (0.51), residues: 89
  loop : -0.23 (0.35), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 386 
 HIS   0.004   0.001   HIS A 665 
 PHE   0.015   0.002   PHE A 960 
 TYR   0.023   0.002   TYR A 904 
 ARG   0.012   0.000   ARG A 777 

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A  278 MET cc_start: 0.4533 (mmp) cc_final: 0.3399 (ttt)
REVERT: A  682 GLN cc_start: 0.6800 (mp-120) cc_final: 0.5785 (mt0)
REVERT: A  926 ASP cc_start: 0.4584 (OUTLIER) cc_final: 0.4346 (t70)
REVERT: A  979 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5202 (mtt-85)
REVERT: A  983 MET cc_start: 0.5360 (ttm) cc_final: 0.4396 (ptt)
  outliers start: 19
  outliers final: 10
  residues processed: 105
  average time/residue: 0.9688
  time to fit residues: 108.8831
Evaluate side-chains
  104 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  810 ASP
Chi-restraints excluded: chain A residue  926 ASP
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 78 optimal weight:    0.2980
   chunk 45 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 637 GLN
** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6079
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7173  Z= 0.245
  Angle     :  0.611   9.120   9696  Z= 0.307
  Chirality :  0.043   0.234   1054
  Planarity :  0.005   0.080   1238
  Dihedral  :  5.183  34.719    943
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.65 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 20.66 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.29), residues: 839
  helix: -0.22 (0.26), residues: 386
  sheet:  0.15 (0.49), residues: 96
  loop : -0.27 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 783 
 HIS   0.003   0.001   HIS A 180 
 PHE   0.016   0.002   PHE A 794 
 TYR   0.030   0.002   TYR A 904 
 ARG   0.013   0.001   ARG A 777 

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A  682 GLN cc_start: 0.6807 (mp-120) cc_final: 0.5799 (mt0)
REVERT: A  926 ASP cc_start: 0.4794 (OUTLIER) cc_final: 0.4425 (t70)
REVERT: A  979 ARG cc_start: 0.6308 (OUTLIER) cc_final: 0.5260 (mtt-85)
REVERT: A  983 MET cc_start: 0.5429 (mtm) cc_final: 0.4429 (ptt)
  outliers start: 16
  outliers final: 11
  residues processed: 100
  average time/residue: 1.0069
  time to fit residues: 107.6428
Evaluate side-chains
  98 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  810 ASP
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  926 ASP
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 84 optimal weight:    0.6980
   chunk 77 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 637 GLN
** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6056
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7173  Z= 0.219
  Angle     :  0.603   9.725   9696  Z= 0.301
  Chirality :  0.043   0.234   1054
  Planarity :  0.005   0.078   1238
  Dihedral  :  5.159  34.122    943
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.05 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 20.66 %
    Favored  : 77.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.29), residues: 839
  helix: -0.19 (0.26), residues: 386
  sheet:  0.27 (0.51), residues: 89
  loop : -0.28 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 783 
 HIS   0.003   0.001   HIS A 554 
 PHE   0.018   0.002   PHE A 794 
 TYR   0.030   0.002   TYR A 904 
 ARG   0.014   0.001   ARG A 777 

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.771 
Fit side-chains
REVERT: A  278 MET cc_start: 0.4031 (mmp) cc_final: 0.3059 (ttm)
REVERT: A  637 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6927 (mp-120)
REVERT: A  682 GLN cc_start: 0.6815 (mp-120) cc_final: 0.5796 (mt0)
REVERT: A  709 MET cc_start: 0.6803 (mmt) cc_final: 0.6252 (mmt)
REVERT: A  926 ASP cc_start: 0.4763 (OUTLIER) cc_final: 0.4462 (t70)
REVERT: A  979 ARG cc_start: 0.6227 (OUTLIER) cc_final: 0.5193 (mtt-85)
REVERT: A  983 MET cc_start: 0.5377 (mtm) cc_final: 0.4392 (ptt)
REVERT: A 1040 MET cc_start: 0.7354 (mpt) cc_final: 0.5805 (mpt)
  outliers start: 17
  outliers final: 13
  residues processed: 101
  average time/residue: 0.9829
  time to fit residues: 106.2822
Evaluate side-chains
  99 residues out of total 784 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  637 GLN
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  810 ASP
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  926 ASP
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0000
   chunk 18 optimal weight:    0.0270
   chunk 67 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0470
   chunk 69 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0050
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.1754

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

Flipped N/Q/H residues before XYZ refinement:
A 450 HIS
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 637 GLN
** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.225821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.200263 restraints weight = 6414.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.4307 rms_B_bonded: 1.24
r_work: 0.4108 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3970 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3955 r_free = 0.3955    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3953 r_free = 0.3953    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3953
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6377
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.197   7173  Z= 0.343
  Angle     :  1.076  59.186   9696  Z= 0.604
  Chirality :  0.047   0.687   1054
  Planarity :  0.005   0.078   1238
  Dihedral  :  5.150  34.092    943
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 14.99
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.05 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 21.05 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.29), residues: 839
  helix: -0.18 (0.26), residues: 386
  sheet:  0.27 (0.51), residues: 89
  loop : -0.28 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 386 
 HIS   0.004   0.001   HIS A 554 
 PHE   0.017   0.002   PHE A 794 
 TYR   0.026   0.002   TYR A 904 
 ARG   0.012   0.000   ARG A 777 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2796.55 seconds
wall clock time: 50 minutes 30.75 seconds (3030.75 seconds total)