Starting phenix.real_space_refine
on Wed Mar  4 14:37:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lxd_30005/03_2026/6lxd_30005.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lxd_30005/03_2026/6lxd_30005.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lxd_30005/03_2026/6lxd_30005.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lxd_30005/03_2026/6lxd_30005.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lxd_30005/03_2026/6lxd_30005.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lxd_30005/03_2026/6lxd_30005.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5612 atoms to isotropic.
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
     Zn      2      6.06       5
     P      72      5.49       5
     S      52      5.16       5
     C    5705      2.51       5
     N    1680      2.21       5
     O    1924      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 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: 9435
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7517
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 918, 7517
          Classifications: {'peptide': 918}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 52, 'TRANS': 865}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 205
          Classifications: {'peptide': 24}
          Link IDs: {'TRANS': 23}
    Chain: "C"
      Number of atoms: 179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 179
          Classifications: {'peptide': 21}
          Link IDs: {'TRANS': 20}
    Chain: "D"
      Number of atoms: 1532
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1532
          Classifications: {'RNA': 72}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 36, 'rna3p_pyr': 32}
          Link IDs: {'rna2p': 4, 'rna3p': 67}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    928  SG  CYS A 561      41.256  73.628 107.458  1.00125.53           S
  ATOM   1886  SG  CYS A 676      43.580  71.223 104.928  1.00125.53           S
  ATOM    736  SG  CYS A 536      57.186  54.545  88.837  1.00135.03           S
  ATOM    751  SG  CYS A 538      58.211  55.298  85.576  1.00158.87           S

  Time building chain proxies: 2.24, per 1000 atoms: 0.24
  Number of scatterers: 9435
  At special positions: 0
  Unit cell: (76.95, 101.25, 145.8, 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)
     Zn      2     29.99
     S      52     16.00
     P      72     15.00
     O    1924      8.00
     N    1680      7.00
     C    5705      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: 0.80
  Conformation dependent library (CDL) restraints added in 414.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1401 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A 676 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A 561 "
        pdb="ZN    ZN A1401 " - pdb=" NE2 HIS A 609 "
        pdb="ZN    ZN A1401 " - pdb=" NE2 HIS A 680 "
      pdb="  ZN A1402 "
        pdb="ZN    ZN A1402 " - pdb=" NE2 HIS A1026 "
        pdb="ZN    ZN A1402 " - pdb=" SG  CYS A 536 "
        pdb="ZN    ZN A1402 " - pdb=" SG  CYS A 538 "
        pdb="ZN    ZN A1402 " - pdb=" NE2 HIS A 549 "
      Number of angles added : 4


  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1836

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 6 sheets defined
      51.3% alpha, 8.1% beta
      26 base pairs and 45 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 439 through 456
      removed outlier: 3.944A  pdb=" N   GLY A 453 " --> pdb=" O   GLU A 449 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   SER A 454 " --> pdb=" O   GLU A 450 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLN A 456 " --> pdb=" O   LEU A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 459
      No H-bonds generated for 'chain 'A' and resid 457 through 459'
    Processing helix  chain 'A' and resid 506 through 511
    Processing helix  chain 'A' and resid 512 through 514
      No H-bonds generated for 'chain 'A' and resid 512 through 514'
    Processing helix  chain 'A' and resid 541 through 545
    Processing helix  chain 'A' and resid 546 through 550
    Processing helix  chain 'A' and resid 641 through 653
      removed outlier: 3.674A  pdb=" N   LEU A 645 " --> pdb=" O   CYS A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 710
    Processing helix  chain 'A' and resid 716 through 726
      removed outlier: 4.485A  pdb=" N   ALA A 720 " --> pdb=" O   GLU A 716 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ASN A 721 " --> pdb=" O   GLU A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 737
    Processing helix  chain 'A' and resid 790 through 803
    Processing helix  chain 'A' and resid 813 through 829
    Processing helix  chain 'A' and resid 856 through 883
      Proline residue:  A 864  - end of helix
    Processing helix  chain 'A' and resid 889 through 897
    Processing helix  chain 'A' and resid 909 through 920
    Processing helix  chain 'A' and resid 930 through 935
    Processing helix  chain 'A' and resid 940 through 951
      removed outlier: 4.175A  pdb=" N   THR A 944 " --> pdb=" O   LYS A 940 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU A 945 " --> pdb=" O   GLY A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 987
    Processing helix  chain 'A' and resid 992 through 1005
      removed outlier: 3.682A  pdb=" N   LEU A 996 " --> pdb=" O   GLU A 992 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLN A1005 " --> pdb=" O   THR A1001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1015
      removed outlier: 4.071A  pdb=" N   LYS A1015 " --> pdb=" O   MET A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1033 through 1055
    Processing helix  chain 'A' and resid 1056 through 1069
    Processing helix  chain 'A' and resid 1074 through 1079
    Processing helix  chain 'A' and resid 1084 through 1089
    Processing helix  chain 'A' and resid 1103 through 1115
      removed outlier: 3.754A  pdb=" N   LEU A1107 " --> pdb=" O   VAL A1103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1129
      removed outlier: 4.177A  pdb=" N   LEU A1124 " --> pdb=" O   HIS A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1166
    Processing helix  chain 'A' and resid 1171 through 1180
      removed outlier: 4.285A  pdb=" N   LEU A1177 " --> pdb=" O   HIS A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1183 through 1195
    Processing helix  chain 'A' and resid 1196 through 1200
    Processing helix  chain 'A' and resid 1213 through 1232
    Processing helix  chain 'A' and resid 1233 through 1253
      removed outlier: 4.045A  pdb=" N   VAL A1237 " --> pdb=" O   ASP A1233 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   PHE A1246 " --> pdb=" O   ASN A1242 " (cutoff:3.500A)
      Proline residue:  A1247  - end of helix
      removed outlier: 4.194A  pdb=" N   LYS A1250 " --> pdb=" O   PHE A1246 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   GLU A1251 " --> pdb=" O   PRO A1247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1260 through 1271
      removed outlier: 4.235A  pdb=" N   LEU A1265 " --> pdb=" O   PRO A1261 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   GLN A1266 " --> pdb=" O   LYS A1262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1316 through 1331
    Processing helix  chain 'A' and resid 1336 through 1348
    Processing helix  chain 'A' and resid 1350 through 1356
    Processing helix  chain 'A' and resid 1356 through 1361
    Processing helix  chain 'A' and resid 1362 through 1364
      No H-bonds generated for 'chain 'A' and resid 1362 through 1364'
    Processing helix  chain 'B' and resid 728 through 750
    Processing helix  chain 'C' and resid 730 through 749
      removed outlier: 3.852A  pdb=" N   LYS C 734 " --> pdb=" O   HIS C 730 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   GLU C 748 " --> pdb=" O   GLU C 744 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR C 749 " --> pdb=" O   GLU C 745 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 423
    Processing sheet with id=AA2, first strand: chain 'A' and resid 591 through 593
      removed outlier: 11.753A  pdb=" N   GLU A 602 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 8.620A  pdb=" N   VAL A 578 " --> pdb=" O   GLU A 602 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   PHE A 604 " --> pdb=" O   ILE A 576 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   CYS A 618 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 591 through 593
      removed outlier: 6.326A  pdb=" N   PHE A 601 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   VAL A 686 " --> pdb=" O   PHE A 601 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   GLY A 603 " --> pdb=" O   ARG A 684 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 751 through 753
      removed outlier: 3.642A  pdb=" N   ILE A 741 " --> pdb=" O   ILE A 852 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ILE A 852 " --> pdb=" O   ILE A 741 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   THR A 743 " --> pdb=" O   THR A 850 " (cutoff:3.500A)
      removed outlier: 5.011A  pdb=" N   THR A 850 " --> pdb=" O   THR A 743 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 756 through 757
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1283 through 1290
      removed outlier: 7.082A  pdb=" N   THR A1299 " --> pdb=" O   LEU A1287 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   THR A1289 " --> pdb=" O   THR A1297 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   THR A1297 " --> pdb=" O   THR A1289 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   TYR A1298 " --> pdb=" O   LYS A1313 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   LYS A1313 " --> pdb=" O   TYR A1298 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   VAL A1300 " --> pdb=" O   CYS A1311 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   CYS A1311 " --> pdb=" O   VAL A1300 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   VAL A1302 " --> pdb=" O   ILE A1309 " (cutoff:3.500A)

    346 hydrogen bonds defined for protein.
    1005 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      63 hydrogen bonds
      106 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      45 stacking parallelities
  Total time for adding SS restraints: 1.63

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2798
        1.34 -     1.46: 1984
        1.46 -     1.58: 4797
        1.58 -     1.70: 142
        1.70 -     1.82: 84
  Bond restraints: 9805
  Sorted by residual:
  bond pdb=" N   CYS A 561 "
       pdb=" CA  CYS A 561 "
    ideal  model  delta    sigma   weight residual
    1.453  1.476 -0.023 1.27e-02 6.20e+03 3.25e+00
  bond pdb=" CA  ARG A 836 "
       pdb=" C   ARG A 836 "
    ideal  model  delta    sigma   weight residual
    1.532  1.521  0.012 9.60e-03 1.09e+04 1.48e+00
  bond pdb=" C   ASP A 855 "
       pdb=" N   VAL A 856 "
    ideal  model  delta    sigma   weight residual
    1.332  1.316  0.016 1.36e-02 5.41e+03 1.42e+00
  bond pdb=" C   VAL A 714 "
       pdb=" N   PRO A 715 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.027 2.34e-02 1.83e+03 1.29e+00
  bond pdb=" N   VAL A 856 "
       pdb=" CA  VAL A 856 "
    ideal  model  delta    sigma   weight residual
    1.459  1.472 -0.013 1.25e-02 6.40e+03 1.09e+00
  ... (remaining 9800 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 13073
        1.24 -     2.47: 402
        2.47 -     3.71: 85
        3.71 -     4.94: 16
        4.94 -     6.18: 16
  Bond angle restraints: 13592
  Sorted by residual:
  angle pdb=" O   VAL A 856 "
        pdb=" C   VAL A 856 "
        pdb=" N   CYS A 857 "
      ideal   model   delta    sigma   weight residual
     122.57  126.02   -3.45 1.25e+00 6.40e-01 7.60e+00
  angle pdb=" N   VAL A 856 "
        pdb=" CA  VAL A 856 "
        pdb=" C   VAL A 856 "
      ideal   model   delta    sigma   weight residual
     109.34  103.65    5.69 2.08e+00 2.31e-01 7.48e+00
  angle pdb=" N   GLU A 823 "
        pdb=" CA  GLU A 823 "
        pdb=" C   GLU A 823 "
      ideal   model   delta    sigma   weight residual
     111.07  108.20    2.87 1.07e+00 8.73e-01 7.17e+00
  angle pdb=" CA  CYS A 561 "
        pdb=" C   CYS A 561 "
        pdb=" O   CYS A 561 "
      ideal   model   delta    sigma   weight residual
     121.88  119.06    2.82 1.13e+00 7.83e-01 6.22e+00
  angle pdb=" N   LEU A 863 "
        pdb=" CA  LEU A 863 "
        pdb=" C   LEU A 863 "
      ideal   model   delta    sigma   weight residual
     109.81  115.22   -5.41 2.21e+00 2.05e-01 5.99e+00
  ... (remaining 13587 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 5277
       17.50 -    35.00: 474
       35.00 -    52.50: 147
       52.50 -    70.00: 104
       70.00 -    87.50: 20
  Dihedral angle restraints: 6022
    sinusoidal: 3194
      harmonic: 2828
  Sorted by residual:
  dihedral pdb=" CA  ARG A 463 "
           pdb=" C   ARG A 463 "
           pdb=" N   PRO A 464 "
           pdb=" CA  PRO A 464 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.73   19.27     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  ALA A 780 "
           pdb=" C   ALA A 780 "
           pdb=" N   GLN A 781 "
           pdb=" CA  GLN A 781 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.97   19.03     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  PRO A 779 "
           pdb=" C   PRO A 779 "
           pdb=" N   ALA A 780 "
           pdb=" CA  ALA A 780 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.46  -18.54     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 6019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1321
       0.054 -    0.107: 187
       0.107 -    0.161: 17
       0.161 -    0.215: 1
       0.215 -    0.269: 1
  Chirality restraints: 1527
  Sorted by residual:
  chirality pdb=" CA  VAL A 856 "
            pdb=" N   VAL A 856 "
            pdb=" C   VAL A 856 "
            pdb=" CB  VAL A 856 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.71   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  CYS A 561 "
            pdb=" N   CYS A 561 "
            pdb=" C   CYS A 561 "
            pdb=" CB  CYS A 561 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.20e-01
  chirality pdb=" CB  THR A 438 "
            pdb=" CA  THR A 438 "
            pdb=" OG1 THR A 438 "
            pdb=" CG2 THR A 438 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.14e-01
  ... (remaining 1524 not shown)

  Planarity restraints: 1495
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D  70 "    0.016 2.00e-02 2.50e+03   1.98e-02 8.83e+00
        pdb=" N1    C D  70 "   -0.013 2.00e-02 2.50e+03
        pdb=" C2    C D  70 "    0.043 2.00e-02 2.50e+03
        pdb=" O2    C D  70 "   -0.032 2.00e-02 2.50e+03
        pdb=" N3    C D  70 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    C D  70 "    0.006 2.00e-02 2.50e+03
        pdb=" N4    C D  70 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    C D  70 "   -0.008 2.00e-02 2.50e+03
        pdb=" C6    C D  70 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1260 "   -0.038 5.00e-02 4.00e+02   5.69e-02 5.17e+00
        pdb=" N   PRO A1261 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A1261 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A1261 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 580 "   -0.035 5.00e-02 4.00e+02   5.26e-02 4.43e+00
        pdb=" N   PRO A 581 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 581 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 581 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1492 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1844
        2.77 -     3.30: 9564
        3.30 -     3.84: 16679
        3.84 -     4.37: 18939
        4.37 -     4.90: 29604
  Nonbonded interactions: 76630
  Sorted by model distance:
  nonbonded pdb=" O2'   G D  35 "
            pdb=" O4'   U D  36 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   ILE A 772 "
            pdb=" OG  SER A 844 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OH  TYR A1024 "
            pdb=" O   LEU A1030 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   ARG A1126 "
            pdb=" OG1 THR A1129 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   LYS A 559 "
            pdb=" NH2 ARG A 570 "
     model   vdw
     2.281 3.120
  ... (remaining 76625 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 729 through 749)
  selection = chain 'C'
}

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:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.990
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
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      :  0.014   0.758   9813  Z= 0.325
  Angle     :  0.669  29.963  13596  Z= 0.311
  Chirality :  0.037   0.269   1527
  Planarity :  0.004   0.057   1495
  Dihedral  : 16.821  87.502   4186
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  5.56 %
    Favored  : 93.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.27 (0.25), residues: 955
  helix: -0.89 (0.22), residues: 440
  sheet: -2.70 (0.53), residues: 76
  loop : -3.51 (0.27), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1248 
 TYR   0.009   0.001   TYR A 784 
 PHE   0.013   0.001   PHE A1252 
 TRP   0.008   0.001   TRP A1258 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 9805)
  covalent geometry    : angle       0.54783 (13592)
  hydrogen bonds       : bond        0.12012 (  407)
  hydrogen bonds       : angle       5.14718 ( 1111)
  metal coordination   : bond        0.47361 (    8)
  metal coordination   : angle      22.39442 (    4)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 162
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  618 CYS cc_start: 0.7720 (t) cc_final: 0.7361 (t)
REVERT: A  856 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8572 (m)
REVERT: A  889 ASP cc_start: 0.8569 (t0) cc_final: 0.8198 (t0)
REVERT: A  933 HIS cc_start: 0.7146 (m90) cc_final: 0.6768 (m90)
REVERT: A 1059 GLU cc_start: 0.8749 (mp0) cc_final: 0.8455 (mp0)
REVERT: A 1111 GLU cc_start: 0.8121 (tt0) cc_final: 0.7891 (tt0)
REVERT: A 1235 GLU cc_start: 0.8301 (mp0) cc_final: 0.7970 (mp0)
REVERT: A 1326 MET cc_start: 0.8582 (ttm) cc_final: 0.7526 (ttp)
REVERT: A 1355 MET cc_start: 0.8495 (mtt) cc_final: 0.8234 (mpp)
REVERT: A 1357 TRP cc_start: 0.6978 (t-100) cc_final: 0.6716 (t-100)
REVERT: B  735 LEU cc_start: 0.9241 (mt) cc_final: 0.8882 (mt)
REVERT: B  742 LEU cc_start: 0.9570 (mm) cc_final: 0.8827 (mm)
REVERT: B  744 GLU cc_start: 0.8552 (pp20) cc_final: 0.7952 (pp20)
REVERT: B  748 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7854 (mm-30)
REVERT: C  735 LEU cc_start: 0.9306 (pp) cc_final: 0.8998 (pp)
REVERT: C  736 GLN cc_start: 0.9240 (tp40) cc_final: 0.8623 (tp40)
REVERT: C  742 LEU cc_start: 0.9163 (tt) cc_final: 0.8925 (tp)
  outliers start: 6
  outliers final: 1
  residues processed: 168
  average time/residue: 0.1238
  time to fit residues: 27.3265
Evaluate side-chains
  101 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  561 CYS
Chi-restraints excluded: chain A residue  856 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0370
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    0.0370
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.8140

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

Flipped N/Q/H residues before XYZ refinement:
** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 624 ASN
A 639 ASN
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 812 GLN
A 888 GLN
** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1087 GLN
A1136 ASN
A1170 HIS
A1184 ASN
A1197 GLN
** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1318 GLN
C 736 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.065298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.053631 restraints weight = 46414.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.055164 restraints weight = 27992.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.056215 restraints weight = 19452.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.056885 restraints weight = 14908.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.057467 restraints weight = 12376.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   9813  Z= 0.123
  Angle     :  0.633   9.843  13596  Z= 0.310
  Chirality :  0.038   0.146   1527
  Planarity :  0.004   0.056   1495
  Dihedral  : 16.833  74.110   2152
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.40 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.27), residues: 955
  helix:  0.17 (0.24), residues: 451
  sheet: -2.66 (0.58), residues: 72
  loop : -3.19 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 687 
 TYR   0.013   0.001   TYR A 733 
 PHE   0.028   0.001   PHE A 762 
 TRP   0.007   0.001   TRP A1258 
 HIS   0.008   0.001   HIS A1026 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9805)
  covalent geometry    : angle       0.62252 (13592)
  hydrogen bonds       : bond        0.03972 (  407)
  hydrogen bonds       : angle       4.39795 ( 1111)
  metal coordination   : bond        0.03543 (    8)
  metal coordination   : angle       6.73145 (    4)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  823 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8560 (mt-10)
REVERT: A 1111 GLU cc_start: 0.7663 (tt0) cc_final: 0.7123 (tm-30)
REVERT: A 1154 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7687 (ttp)
REVERT: A 1196 MET cc_start: 0.7729 (ptp) cc_final: 0.7496 (mtt)
REVERT: A 1355 MET cc_start: 0.8327 (mtt) cc_final: 0.7840 (mmm)
REVERT: B  735 LEU cc_start: 0.9041 (mt) cc_final: 0.8402 (mt)
REVERT: B  744 GLU cc_start: 0.8454 (pp20) cc_final: 0.7900 (pp20)
REVERT: B  748 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7823 (mm-30)
REVERT: C  735 LEU cc_start: 0.9219 (pp) cc_final: 0.8969 (pp)
  outliers start: 16
  outliers final: 10
  residues processed: 127
  average time/residue: 0.1091
  time to fit residues: 18.9895
Evaluate side-chains
  105 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  823 GLU
Chi-restraints excluded: chain A residue  891 CYS
Chi-restraints excluded: chain A residue 1036 LEU
Chi-restraints excluded: chain A residue 1116 VAL
Chi-restraints excluded: chain A residue 1154 MET
Chi-restraints excluded: chain A residue 1309 ILE
Chi-restraints excluded: chain C residue  730 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 94 optimal weight:    9.9990
   chunk 93 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 52 optimal weight:    9.9990
   chunk 98 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0060
   chunk 43 optimal weight:    5.9990
   overall best weight:    1.9602

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

Flipped N/Q/H residues before XYZ refinement:
** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 919 ASN
A1256 GLN
** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 736 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.062421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.050966 restraints weight = 47282.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.052396 restraints weight = 28456.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.053415 restraints weight = 19846.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.054143 restraints weight = 15230.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.054574 restraints weight = 12542.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9813  Z= 0.160
  Angle     :  0.641  10.092  13596  Z= 0.319
  Chirality :  0.039   0.161   1527
  Planarity :  0.005   0.061   1495
  Dihedral  : 16.745  74.123   2150
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.90 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.41 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.27), residues: 955
  helix:  0.29 (0.24), residues: 459
  sheet: -2.49 (0.57), residues: 72
  loop : -3.09 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 961 
 TYR   0.013   0.001   TYR A 733 
 PHE   0.046   0.002   PHE A1252 
 TRP   0.022   0.002   TRP A 725 
 HIS   0.006   0.001   HIS A 899 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 9805)
  covalent geometry    : angle       0.62891 (13592)
  hydrogen bonds       : bond        0.04362 (  407)
  hydrogen bonds       : angle       4.41576 ( 1111)
  metal coordination   : bond        0.02880 (    8)
  metal coordination   : angle       7.29414 (    4)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  522 LEU cc_start: 0.7843 (mm) cc_final: 0.7282 (pp)
REVERT: A  573 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.6680 (t-90)
REVERT: A  823 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8494 (mt-10)
REVERT: A 1111 GLU cc_start: 0.7886 (tt0) cc_final: 0.7683 (tt0)
REVERT: A 1154 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7736 (ttp)
REVERT: A 1241 MET cc_start: 0.8622 (mmm) cc_final: 0.8154 (mmm)
REVERT: A 1260 ASP cc_start: 0.6971 (t0) cc_final: 0.6612 (t0)
REVERT: A 1329 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8576 (pp)
REVERT: B  737 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8837 (mm-30)
REVERT: B  738 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8752 (mm-30)
REVERT: B  748 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7838 (mm-30)
REVERT: C  740 LYS cc_start: 0.9374 (tptm) cc_final: 0.9063 (ttpp)
  outliers start: 26
  outliers final: 15
  residues processed: 118
  average time/residue: 0.1114
  time to fit residues: 17.9055
Evaluate side-chains
  105 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  561 CYS
Chi-restraints excluded: chain A residue  573 HIS
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  823 GLU
Chi-restraints excluded: chain A residue  891 CYS
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1022 MET
Chi-restraints excluded: chain A residue 1036 LEU
Chi-restraints excluded: chain A residue 1116 VAL
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1148 PHE
Chi-restraints excluded: chain A residue 1154 MET
Chi-restraints excluded: chain A residue 1309 ILE
Chi-restraints excluded: chain A residue 1329 LEU
Chi-restraints excluded: chain B residue  742 LEU
Chi-restraints excluded: chain C residue  730 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   chunk 43 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 97 optimal weight:   10.0000
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 791 GLN
A1120 HIS
A1256 GLN
** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.063256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.051377 restraints weight = 48427.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.052819 restraints weight = 29614.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.053823 restraints weight = 20870.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.054507 restraints weight = 16277.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.054972 restraints weight = 13622.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9813  Z= 0.137
  Angle     :  0.632  10.746  13596  Z= 0.313
  Chirality :  0.039   0.147   1527
  Planarity :  0.004   0.062   1495
  Dihedral  : 16.693  74.091   2150
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 17.38 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.28), residues: 955
  helix:  0.54 (0.25), residues: 457
  sheet: -2.29 (0.58), residues: 72
  loop : -2.93 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 687 
 TYR   0.013   0.001   TYR A 733 
 PHE   0.025   0.001   PHE A1252 
 TRP   0.048   0.002   TRP A 725 
 HIS   0.005   0.001   HIS A1026 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9805)
  covalent geometry    : angle       0.62370 (13592)
  hydrogen bonds       : bond        0.03914 (  407)
  hydrogen bonds       : angle       4.32312 ( 1111)
  metal coordination   : bond        0.02400 (    8)
  metal coordination   : angle       6.02652 (    4)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  902 HIS cc_start: 0.5779 (OUTLIER) cc_final: 0.5574 (t-90)
REVERT: A 1111 GLU cc_start: 0.7771 (tt0) cc_final: 0.7512 (tt0)
REVERT: A 1225 ILE cc_start: 0.9448 (pt) cc_final: 0.9123 (tt)
REVERT: A 1241 MET cc_start: 0.8483 (mmm) cc_final: 0.8149 (mmm)
REVERT: A 1329 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8654 (pp)
REVERT: B  737 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8527 (mm-30)
REVERT: B  738 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8729 (mm-30)
REVERT: B  740 LYS cc_start: 0.8678 (ptmm) cc_final: 0.7993 (ptpp)
REVERT: B  748 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7850 (mm-30)
REVERT: C  735 LEU cc_start: 0.9114 (pp) cc_final: 0.8875 (pp)
  outliers start: 28
  outliers final: 17
  residues processed: 120
  average time/residue: 0.1071
  time to fit residues: 17.7674
Evaluate side-chains
  105 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  561 CYS
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  862 MET
Chi-restraints excluded: chain A residue  891 CYS
Chi-restraints excluded: chain A residue  902 HIS
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1116 VAL
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1148 PHE
Chi-restraints excluded: chain A residue 1243 VAL
Chi-restraints excluded: chain A residue 1256 GLN
Chi-restraints excluded: chain A residue 1309 ILE
Chi-restraints excluded: chain A residue 1329 LEU
Chi-restraints excluded: chain B residue  742 LEU
Chi-restraints excluded: chain C residue  730 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0040
   chunk 90 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 79 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 98 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   overall best weight:    1.8000

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

Flipped N/Q/H residues before XYZ refinement:
** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 525 ASN
** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1256 GLN
** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 736 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.062830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.051330 restraints weight = 48742.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.052781 restraints weight = 29624.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.053811 restraints weight = 20731.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.054452 restraints weight = 15959.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.054983 restraints weight = 13317.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9813  Z= 0.147
  Angle     :  0.629   9.150  13596  Z= 0.315
  Chirality :  0.039   0.152   1527
  Planarity :  0.004   0.054   1495
  Dihedral  : 16.642  74.151   2150
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.90 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.84 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.28), residues: 955
  helix:  0.47 (0.25), residues: 465
  sheet: -2.12 (0.58), residues: 72
  loop : -2.89 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 967 
 TYR   0.014   0.001   TYR A 733 
 PHE   0.049   0.002   PHE A1252 
 TRP   0.053   0.002   TRP A 725 
 HIS   0.005   0.001   HIS A1026 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9805)
  covalent geometry    : angle       0.61958 (13592)
  hydrogen bonds       : bond        0.04077 (  407)
  hydrogen bonds       : angle       4.37320 ( 1111)
  metal coordination   : bond        0.02230 (    8)
  metal coordination   : angle       6.23551 (    4)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 96
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  514 HIS cc_start: 0.4575 (m-70) cc_final: 0.4334 (m-70)
REVERT: A  573 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.6760 (t-90)
REVERT: A  902 HIS cc_start: 0.6321 (OUTLIER) cc_final: 0.5911 (t-90)
REVERT: A  977 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7399 (mt-10)
REVERT: A 1111 GLU cc_start: 0.7713 (tt0) cc_final: 0.7455 (tt0)
REVERT: A 1154 MET cc_start: 0.8010 (ptp) cc_final: 0.7519 (ttp)
REVERT: A 1225 ILE cc_start: 0.9450 (pt) cc_final: 0.9092 (tt)
REVERT: A 1241 MET cc_start: 0.8383 (mmm) cc_final: 0.8066 (mmm)
REVERT: A 1329 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8732 (pp)
REVERT: A 1355 MET cc_start: 0.8047 (mtt) cc_final: 0.7685 (mmt)
REVERT: B  735 LEU cc_start: 0.9392 (mt) cc_final: 0.8763 (mm)
REVERT: B  737 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8471 (mm-30)
REVERT: B  740 LYS cc_start: 0.8678 (ptmm) cc_final: 0.7969 (ptpp)
REVERT: B  748 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7843 (mm-30)
REVERT: C  740 LYS cc_start: 0.9391 (tptm) cc_final: 0.9074 (ttpp)
  outliers start: 31
  outliers final: 19
  residues processed: 122
  average time/residue: 0.1013
  time to fit residues: 17.2339
Evaluate side-chains
  108 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  561 CYS
Chi-restraints excluded: chain A residue  573 HIS
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  862 MET
Chi-restraints excluded: chain A residue  891 CYS
Chi-restraints excluded: chain A residue  902 HIS
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1148 PHE
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1243 VAL
Chi-restraints excluded: chain A residue 1309 ILE
Chi-restraints excluded: chain A residue 1329 LEU
Chi-restraints excluded: chain B residue  736 GLN
Chi-restraints excluded: chain B residue  742 LEU
Chi-restraints excluded: chain C residue  730 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 86 optimal weight:    0.0020
   chunk 45 optimal weight:    0.1980
   chunk 77 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0030
   chunk 19 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   chunk 88 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.4400

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1242 ASN
A1266 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.065008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.053110 restraints weight = 47638.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.054576 restraints weight = 29124.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.055614 restraints weight = 20484.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.056308 restraints weight = 15877.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.056803 restraints weight = 13264.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9813  Z= 0.111
  Angle     :  0.637  13.588  13596  Z= 0.311
  Chirality :  0.039   0.166   1527
  Planarity :  0.004   0.054   1495
  Dihedral  : 16.577  74.063   2150
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 19.24 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.28), residues: 955
  helix:  0.58 (0.25), residues: 461
  sheet: -2.13 (0.57), residues: 72
  loop : -2.70 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 517 
 TYR   0.011   0.001   TYR A 784 
 PHE   0.042   0.001   PHE A1252 
 TRP   0.054   0.002   TRP A 725 
 HIS   0.004   0.001   HIS A1026 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9805)
  covalent geometry    : angle       0.63206 (13592)
  hydrogen bonds       : bond        0.03509 (  407)
  hydrogen bonds       : angle       4.21566 ( 1111)
  metal coordination   : bond        0.02203 (    8)
  metal coordination   : angle       4.85775 (    4)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  514 HIS cc_start: 0.4304 (m-70) cc_final: 0.4062 (m-70)
REVERT: A  902 HIS cc_start: 0.5854 (OUTLIER) cc_final: 0.5494 (t-90)
REVERT: A  908 MET cc_start: 0.7563 (tmm) cc_final: 0.6974 (tmm)
REVERT: A  977 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7386 (mt-10)
REVERT: A 1004 VAL cc_start: 0.8889 (p) cc_final: 0.8669 (p)
REVERT: A 1111 GLU cc_start: 0.7699 (tt0) cc_final: 0.7457 (tt0)
REVERT: A 1154 MET cc_start: 0.7993 (ptp) cc_final: 0.7435 (ttp)
REVERT: A 1225 ILE cc_start: 0.9427 (pt) cc_final: 0.9069 (tt)
REVERT: A 1241 MET cc_start: 0.8186 (mmm) cc_final: 0.7872 (mmm)
REVERT: A 1329 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8762 (pp)
REVERT: A 1355 MET cc_start: 0.8104 (mtt) cc_final: 0.7612 (mmt)
REVERT: B  735 LEU cc_start: 0.9270 (mt) cc_final: 0.9053 (mm)
REVERT: B  737 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8835 (mm-30)
REVERT: B  748 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7864 (mm-30)
REVERT: C  735 LEU cc_start: 0.9161 (pp) cc_final: 0.8763 (tt)
REVERT: C  740 LYS cc_start: 0.9379 (tptm) cc_final: 0.9108 (ttpp)
  outliers start: 24
  outliers final: 18
  residues processed: 118
  average time/residue: 0.1001
  time to fit residues: 16.5086
Evaluate side-chains
  111 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  561 CYS
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  862 MET
Chi-restraints excluded: chain A residue  891 CYS
Chi-restraints excluded: chain A residue  902 HIS
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1116 VAL
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1148 PHE
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1309 ILE
Chi-restraints excluded: chain A residue 1329 LEU
Chi-restraints excluded: chain B residue  742 LEU
Chi-restraints excluded: chain C residue  730 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 38 optimal weight:    0.3980
   chunk 75 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 94 optimal weight:    9.9990
   chunk 11 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    2.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 902 HIS
A1256 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.061132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.049946 restraints weight = 48083.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.051346 restraints weight = 28883.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.052371 restraints weight = 20214.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.053077 restraints weight = 15505.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.053505 restraints weight = 12772.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9813  Z= 0.189
  Angle     :  0.713  10.990  13596  Z= 0.352
  Chirality :  0.041   0.179   1527
  Planarity :  0.005   0.050   1495
  Dihedral  : 16.613  74.272   2150
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.42 %
    Favored  : 90.58 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.93 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.27), residues: 955
  helix:  0.33 (0.24), residues: 466
  sheet: -2.00 (0.58), residues: 72
  loop : -2.73 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 967 
 TYR   0.015   0.002   TYR A 733 
 PHE   0.026   0.002   PHE A1252 
 TRP   0.051   0.002   TRP A 725 
 HIS   0.005   0.001   HIS A1026 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 9805)
  covalent geometry    : angle       0.70514 (13592)
  hydrogen bonds       : bond        0.04578 (  407)
  hydrogen bonds       : angle       4.59498 ( 1111)
  metal coordination   : bond        0.01990 (    8)
  metal coordination   : angle       6.36853 (    4)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  514 HIS cc_start: 0.4404 (m-70) cc_final: 0.4200 (m-70)
REVERT: A  977 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7384 (mt-10)
REVERT: A 1154 MET cc_start: 0.8055 (ptp) cc_final: 0.7595 (ttp)
REVERT: A 1225 ILE cc_start: 0.9444 (pt) cc_final: 0.9124 (tt)
REVERT: A 1241 MET cc_start: 0.8486 (mmm) cc_final: 0.8138 (mmm)
REVERT: A 1329 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8776 (pp)
REVERT: A 1355 MET cc_start: 0.8184 (mtt) cc_final: 0.7731 (mmm)
REVERT: B  737 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8806 (mm-30)
REVERT: B  742 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9337 (mm)
REVERT: B  748 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7861 (mm-30)
REVERT: C  740 LYS cc_start: 0.9385 (tptm) cc_final: 0.9103 (ttpp)
  outliers start: 28
  outliers final: 19
  residues processed: 111
  average time/residue: 0.1016
  time to fit residues: 15.6661
Evaluate side-chains
  104 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  561 CYS
Chi-restraints excluded: chain A residue  600 ILE
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  862 MET
Chi-restraints excluded: chain A residue  891 CYS
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue  964 HIS
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1148 PHE
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1243 VAL
Chi-restraints excluded: chain A residue 1256 GLN
Chi-restraints excluded: chain A residue 1309 ILE
Chi-restraints excluded: chain A residue 1329 LEU
Chi-restraints excluded: chain B residue  742 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 64 optimal weight:    0.3980
   chunk 81 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0770
   chunk 69 optimal weight:    9.9990
   chunk 91 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 95 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.2942

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

Flipped N/Q/H residues before XYZ refinement:
** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1256 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.062743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.051312 restraints weight = 48351.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.052712 restraints weight = 29371.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.053766 restraints weight = 20732.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.054400 restraints weight = 16017.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.054763 restraints weight = 13395.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9813  Z= 0.133
  Angle     :  0.709  13.420  13596  Z= 0.344
  Chirality :  0.042   0.434   1527
  Planarity :  0.004   0.048   1495
  Dihedral  : 16.584  74.149   2150
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.28 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.28), residues: 955
  helix:  0.45 (0.25), residues: 466
  sheet: -1.93 (0.58), residues: 72
  loop : -2.68 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 967 
 TYR   0.013   0.001   TYR A 999 
 PHE   0.023   0.001   PHE A 669 
 TRP   0.051   0.002   TRP A 725 
 HIS   0.005   0.001   HIS A1026 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9805)
  covalent geometry    : angle       0.70221 (13592)
  hydrogen bonds       : bond        0.03967 (  407)
  hydrogen bonds       : angle       4.45509 ( 1111)
  metal coordination   : bond        0.02216 (    8)
  metal coordination   : angle       5.61125 (    4)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 90
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  514 HIS cc_start: 0.4299 (m-70) cc_final: 0.4074 (m-70)
REVERT: A  573 HIS cc_start: 0.7576 (OUTLIER) cc_final: 0.6775 (t-90)
REVERT: A  977 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7326 (mt-10)
REVERT: A 1111 GLU cc_start: 0.7662 (tt0) cc_final: 0.7300 (tp30)
REVERT: A 1154 MET cc_start: 0.8114 (ptp) cc_final: 0.7654 (ttp)
REVERT: A 1225 ILE cc_start: 0.9438 (pt) cc_final: 0.9120 (tt)
REVERT: A 1241 MET cc_start: 0.8329 (mmm) cc_final: 0.8046 (mmm)
REVERT: A 1329 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8747 (pp)
REVERT: B  737 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8496 (mm-30)
REVERT: B  740 LYS cc_start: 0.8719 (ptmm) cc_final: 0.8037 (ptpp)
REVERT: B  748 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7874 (mm-30)
REVERT: C  740 LYS cc_start: 0.9382 (tptm) cc_final: 0.9093 (ttpp)
  outliers start: 28
  outliers final: 19
  residues processed: 114
  average time/residue: 0.0989
  time to fit residues: 15.8893
Evaluate side-chains
  107 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  561 CYS
Chi-restraints excluded: chain A residue  573 HIS
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  862 MET
Chi-restraints excluded: chain A residue  891 CYS
Chi-restraints excluded: chain A residue  920 CYS
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1148 PHE
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1243 VAL
Chi-restraints excluded: chain A residue 1256 GLN
Chi-restraints excluded: chain A residue 1309 ILE
Chi-restraints excluded: chain A residue 1329 LEU
Chi-restraints excluded: chain C residue  729 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 54 optimal weight:    8.9990
   chunk 56 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 37 optimal weight:   10.0000
   chunk 48 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0980
   chunk 8 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1256 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.062791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.051093 restraints weight = 47804.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.052547 restraints weight = 28877.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.053572 restraints weight = 20274.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.054296 restraints weight = 15684.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.054678 restraints weight = 13001.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9813  Z= 0.133
  Angle     :  0.725  14.255  13596  Z= 0.348
  Chirality :  0.042   0.396   1527
  Planarity :  0.004   0.047   1495
  Dihedral  : 16.531  74.157   2150
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 21.32 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.28), residues: 955
  helix:  0.47 (0.25), residues: 466
  sheet: -1.85 (0.59), residues: 72
  loop : -2.64 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 967 
 TYR   0.011   0.001   TYR A 784 
 PHE   0.025   0.001   PHE A 669 
 TRP   0.051   0.002   TRP A 725 
 HIS   0.004   0.001   HIS A1026 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9805)
  covalent geometry    : angle       0.71890 (13592)
  hydrogen bonds       : bond        0.03958 (  407)
  hydrogen bonds       : angle       4.45857 ( 1111)
  metal coordination   : bond        0.02129 (    8)
  metal coordination   : angle       5.56907 (    4)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  514 HIS cc_start: 0.4648 (m-70) cc_final: 0.4382 (m-70)
REVERT: A  573 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.6807 (t-90)
REVERT: A  977 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7325 (mt-10)
REVERT: A 1111 GLU cc_start: 0.7747 (tt0) cc_final: 0.7166 (tm-30)
REVERT: A 1118 PHE cc_start: 0.6547 (m-10) cc_final: 0.6097 (m-10)
REVERT: A 1154 MET cc_start: 0.8128 (ptp) cc_final: 0.7654 (ttp)
REVERT: A 1196 MET cc_start: 0.8029 (mtt) cc_final: 0.7406 (mpp)
REVERT: A 1225 ILE cc_start: 0.9437 (pt) cc_final: 0.9127 (tt)
REVERT: A 1241 MET cc_start: 0.8395 (mmm) cc_final: 0.8155 (mmm)
REVERT: A 1329 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8818 (pp)
REVERT: B  748 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7857 (mm-30)
REVERT: C  740 LYS cc_start: 0.9394 (tptm) cc_final: 0.9085 (ttpp)
  outliers start: 24
  outliers final: 19
  residues processed: 110
  average time/residue: 0.1020
  time to fit residues: 15.7731
Evaluate side-chains
  107 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  561 CYS
Chi-restraints excluded: chain A residue  573 HIS
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  862 MET
Chi-restraints excluded: chain A residue  891 CYS
Chi-restraints excluded: chain A residue  920 CYS
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1148 PHE
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1243 VAL
Chi-restraints excluded: chain A residue 1256 GLN
Chi-restraints excluded: chain A residue 1309 ILE
Chi-restraints excluded: chain A residue 1329 LEU
Chi-restraints excluded: chain C residue  729 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 100 optimal weight:   10.0000
   chunk 88 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0980
   chunk 92 optimal weight:    1.9990
   overall best weight:    2.4188

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

Flipped N/Q/H residues before XYZ refinement:
** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 826 GLN
** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1256 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.061153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.049635 restraints weight = 48560.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.051024 restraints weight = 29469.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.052004 restraints weight = 20818.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.052660 restraints weight = 16195.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.053074 restraints weight = 13592.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9813  Z= 0.184
  Angle     :  0.781  14.289  13596  Z= 0.378
  Chirality :  0.044   0.331   1527
  Planarity :  0.005   0.047   1495
  Dihedral  : 16.506  74.218   2150
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 21.55 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.28), residues: 955
  helix:  0.32 (0.25), residues: 467
  sheet: -1.80 (0.59), residues: 72
  loop : -2.66 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 967 
 TYR   0.014   0.002   TYR A 784 
 PHE   0.030   0.002   PHE A1252 
 TRP   0.050   0.003   TRP A 725 
 HIS   0.005   0.001   HIS A1026 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 9805)
  covalent geometry    : angle       0.77353 (13592)
  hydrogen bonds       : bond        0.04464 (  407)
  hydrogen bonds       : angle       4.65594 ( 1111)
  metal coordination   : bond        0.02034 (    8)
  metal coordination   : angle       6.39216 (    4)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  514 HIS cc_start: 0.4683 (m-70) cc_final: 0.4419 (m-70)
REVERT: A  573 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.7201 (t-90)
REVERT: A  949 MET cc_start: 0.8681 (mtp) cc_final: 0.8445 (mtp)
REVERT: A  977 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7368 (mt-10)
REVERT: A 1111 GLU cc_start: 0.7792 (tt0) cc_final: 0.7217 (tm-30)
REVERT: A 1118 PHE cc_start: 0.6754 (m-10) cc_final: 0.5945 (m-10)
REVERT: A 1154 MET cc_start: 0.8157 (ptp) cc_final: 0.7726 (ttp)
REVERT: A 1225 ILE cc_start: 0.9449 (pt) cc_final: 0.9161 (tt)
REVERT: A 1241 MET cc_start: 0.8494 (mmm) cc_final: 0.8191 (mmm)
REVERT: A 1329 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8775 (pp)
REVERT: B  748 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7864 (mm-30)
  outliers start: 25
  outliers final: 20
  residues processed: 111
  average time/residue: 0.1005
  time to fit residues: 15.7378
Evaluate side-chains
  106 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  561 CYS
Chi-restraints excluded: chain A residue  573 HIS
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  714 VAL
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  862 MET
Chi-restraints excluded: chain A residue  891 CYS
Chi-restraints excluded: chain A residue  920 CYS
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1148 PHE
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1243 VAL
Chi-restraints excluded: chain A residue 1256 GLN
Chi-restraints excluded: chain A residue 1309 ILE
Chi-restraints excluded: chain A residue 1329 LEU
Chi-restraints excluded: chain C residue  729 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 45 optimal weight:    0.3980
   chunk 56 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   chunk 20 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1256 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.062663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.051010 restraints weight = 47284.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.052440 restraints weight = 28700.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.053453 restraints weight = 20177.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.054157 restraints weight = 15642.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.054629 restraints weight = 13013.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9813  Z= 0.132
  Angle     :  0.767  14.749  13596  Z= 0.366
  Chirality :  0.043   0.320   1527
  Planarity :  0.004   0.050   1495
  Dihedral  : 16.467  74.135   2150
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 21.90 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.28), residues: 955
  helix:  0.35 (0.25), residues: 467
  sheet: -1.75 (0.60), residues: 72
  loop : -2.65 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 517 
 TYR   0.012   0.001   TYR A 784 
 PHE   0.027   0.001   PHE A1252 
 TRP   0.050   0.002   TRP A 725 
 HIS   0.005   0.001   HIS A1026 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9805)
  covalent geometry    : angle       0.76150 (13592)
  hydrogen bonds       : bond        0.04050 (  407)
  hydrogen bonds       : angle       4.54873 ( 1111)
  metal coordination   : bond        0.02268 (    8)
  metal coordination   : angle       5.34239 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1470.55 seconds
wall clock time: 26 minutes 12.21 seconds (1572.21 seconds total)