Starting phenix.real_space_refine
on Wed Feb  4 20:33:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wa9_65809/02_2026/9wa9_65809.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wa9_65809/02_2026/9wa9_65809.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wa9_65809/02_2026/9wa9_65809.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wa9_65809/02_2026/9wa9_65809.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wa9_65809/02_2026/9wa9_65809.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wa9_65809/02_2026/9wa9_65809.map"
  }
  resolution = 4.12
  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=   0.003 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     148      5.49       5
     S      22      5.16       5
     C    7560      2.51       5
     N    2272      2.21       5
     O    2786      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12788
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9610
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1171, 9599
          Classifications: {'peptide': 1171}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 1141}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 1171, 9599
          Classifications: {'peptide': 1171}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 1141}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 9755
    Chain: "B"
      Number of atoms: 761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 761
          Classifications: {'DNA': 37}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 36}
    Chain: "C"
      Number of atoms: 286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 286
          Classifications: {'DNA': 14}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 13}
    Chain: "D"
      Number of atoms: 2131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 2131
          Classifications: {'RNA': 100}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 49, 'rna3p_pyr': 40}
          Link IDs: {'rna2p': 11, 'rna3p': 88}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 783 " occ=0.72
      ... (20 atoms not shown)
      pdb=" NH2BARG A 783 " occ=0.28
  Time building chain proxies: 4.76, per 1000 atoms: 0.37
  Number of scatterers: 12788
  At special positions: 0
  Unit cell: (122.436, 114.918, 112.77, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      22     16.00
     P     148     15.00
     O    2786      8.00
     N    2272      7.00
     C    7560      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: 1.16
  Conformation dependent library (CDL) restraints added in 795.7 milliseconds
  

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2228

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 8 sheets defined
      56.3% alpha, 7.5% beta
      56 base pairs and 98 stacking pairs defined.
    Time for finding SS restraints: 1.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 91
      removed outlier: 4.194A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.716A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.504A  pdb=" N   PHE A 164 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 306
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.771A  pdb=" N   ALA A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 353
      removed outlier: 3.537A  pdb=" N   ASP A 353 " --> pdb=" O   GLU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 383
      Proline residue:  A 378  - end of helix
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.512A  pdb=" N   ASN A 407 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.223A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 446
      removed outlier: 3.802A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   GLU A 438 " --> pdb=" O   LYS A 434 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   LYS A 439 " --> pdb=" O   ASP A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 482
      removed outlier: 3.618A  pdb=" N   VAL A 482 " --> pdb=" O   PHE A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 495
      removed outlier: 4.416A  pdb=" N   MET A 495 " --> pdb=" O   PHE A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 3.862A  pdb=" N   LYS A 526 " --> pdb=" O   ASN A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 561 through 568
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 603 through 609
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 629 through 636
      removed outlier: 3.891A  pdb=" N   LEU A 636 " --> pdb=" O   ILE A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 640
    Processing helix  chain 'A' and resid 644 through 654
    Processing helix  chain 'A' and resid 663 through 669
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 698
    Processing helix  chain 'A' and resid 703 through 712
    Processing helix  chain 'A' and resid 719 through 726
    Processing helix  chain 'A' and resid 730 through 752
      removed outlier: 3.712A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLY A 752 " --> pdb=" O   VAL A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 778
      removed outlier: 3.574A  pdb=" N   GLY A 773 " --> pdb=" O   THR A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 792
    Processing helix  chain 'A' and resid 794 through 799
    Processing helix  chain 'A' and resid 802 through 808
      removed outlier: 3.784A  pdb=" N   ASN A 808 " --> pdb=" O   THR A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 818
      removed outlier: 3.513A  pdb=" N   TYR A 812 " --> pdb=" O   ASN A 808 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASN A 818 " --> pdb=" O   TYR A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 831 through 836
      removed outlier: 4.238A  pdb=" N   ASP A 835 " --> pdb=" O   ASN A 831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 859 through 866
      removed outlier: 3.788A  pdb=" N   LYS A 866 " --> pdb=" O   LYS A 862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 872 through 890
      removed outlier: 4.935A  pdb=" N   ASN A 881 " --> pdb=" O   LYS A 877 " (cutoff:3.500A)
      removed outlier: 5.432A  pdb=" N   TYR A 882 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 906
      removed outlier: 4.477A  pdb=" N   ALA A 903 " --> pdb=" O   ASN A 899 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   GLU A 904 " --> pdb=" O   LEU A 900 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 914
    Processing helix  chain 'A' and resid 917 through 927
      removed outlier: 3.798A  pdb=" N   LEU A 921 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 927 through 940
      removed outlier: 3.800A  pdb=" N   VAL A 931 " --> pdb=" O   ILE A 927 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASN A 940 " --> pdb=" O   ASP A 936 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 970
      removed outlier: 4.057A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 998
      removed outlier: 3.502A  pdb=" N   ILE A 998 " --> pdb=" O   GLY A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1087
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
    Processing helix  chain 'A' and resid 1177 through 1186
    Processing helix  chain 'A' and resid 1191 through 1195
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1241
    Processing helix  chain 'A' and resid 1248 through 1262
    Processing helix  chain 'A' and resid 1264 through 1281
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1317
      removed outlier: 3.518A  pdb=" N   PHE A1313 " --> pdb=" O   ILE A1309 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   THR A1314 " --> pdb=" O   ILE A1310 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   LEU A1315 " --> pdb=" O   HIS A1311 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   THR A1316 " --> pdb=" O   LEU A1312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1341 through 1344
      removed outlier: 3.529A  pdb=" N   ASP A1344 " --> pdb=" O   GLU A1341 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1341 through 1344'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 955
      removed outlier: 4.049A  pdb=" N   ILE A 759 " --> pdb=" O   LYS A 954 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   ASN A 758 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   ILE A  48 " --> pdb=" O   ASN A1093 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   VAL A1095 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   ALA A  50 " --> pdb=" O   VAL A1095 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33
      removed outlier: 3.536A  pdb=" N   ILE A  43 " --> pdb=" O   PHE A  32 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36
      removed outlier: 3.679A  pdb=" N   HIS A1349 " --> pdb=" O   THR A1358 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ILE A1348 " --> pdb=" O   LEU A1203 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   LEU A1214 " --> pdb=" O   GLN A1221 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLN A1221 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLU A1219 " --> pdb=" O   SER A1216 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA5, first strand: chain 'A' and resid 559 through 560
      removed outlier: 4.683A  pdb=" N   VAL A 559 " --> pdb=" O   PHE A 587 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 837 through 840
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1139 through 1151
      removed outlier: 3.518A  pdb=" N   VAL A1143 " --> pdb=" O   LEU A1164 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1326
      removed outlier: 3.898A  pdb=" N   PHE A1324 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)

    445 hydrogen bonds defined for protein.
    1300 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      140 hydrogen bonds
      268 hydrogen bond angles
      0 basepair planarities
      56 basepair parallelities
      98 stacking parallelities
  Total time for adding SS restraints: 3.35

  Time building geometry restraints manager: 1.52 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2670
        1.33 -     1.45: 3618
        1.45 -     1.57: 6713
        1.57 -     1.69: 296
        1.69 -     1.81: 42
  Bond restraints: 13339
  Sorted by residual:
  bond pdb=" CA  VAL A 760 "
       pdb=" CB  VAL A 760 "
    ideal  model  delta    sigma   weight residual
    1.540  1.557 -0.017 1.36e-02 5.41e+03 1.61e+00
  bond pdb=" CB  VAL A 760 "
       pdb=" CG1 VAL A 760 "
    ideal  model  delta    sigma   weight residual
    1.521  1.559 -0.038 3.30e-02 9.18e+02 1.31e+00
  bond pdb=" N   VAL A 760 "
       pdb=" CA  VAL A 760 "
    ideal  model  delta    sigma   weight residual
    1.459  1.473 -0.014 1.25e-02 6.40e+03 1.24e+00
  bond pdb=" CA  VAL A 760 "
       pdb=" C   VAL A 760 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.014 1.27e-02 6.20e+03 1.18e+00
  bond pdb=" CD  GLN A 933 "
       pdb=" OE1 GLN A 933 "
    ideal  model  delta    sigma   weight residual
    1.231  1.211  0.020 1.90e-02 2.77e+03 1.09e+00
  ... (remaining 13334 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 18314
        1.72 -     3.45: 299
        3.45 -     5.17: 31
        5.17 -     6.89: 9
        6.89 -     8.62: 3
  Bond angle restraints: 18656
  Sorted by residual:
  angle pdb=" CA  VAL A 760 "
        pdb=" CB  VAL A 760 "
        pdb=" CG1 VAL A 760 "
      ideal   model   delta    sigma   weight residual
     110.40  116.96   -6.56 1.70e+00 3.46e-01 1.49e+01
  angle pdb=" N   GLN A 933 "
        pdb=" CA  GLN A 933 "
        pdb=" CB  GLN A 933 "
      ideal   model   delta    sigma   weight residual
     110.28  116.11   -5.83 1.55e+00 4.16e-01 1.41e+01
  angle pdb=" CA  ARG A  71 "
        pdb=" CB  ARG A  71 "
        pdb=" CG  ARG A  71 "
      ideal   model   delta    sigma   weight residual
     114.10  121.46   -7.36 2.00e+00 2.50e-01 1.35e+01
  angle pdb=" C   ILE A 759 "
        pdb=" N   VAL A 760 "
        pdb=" CA  VAL A 760 "
      ideal   model   delta    sigma   weight residual
     121.97  128.44   -6.47 1.80e+00 3.09e-01 1.29e+01
  angle pdb=" C   GLN A 926 "
        pdb=" N   ILE A 927 "
        pdb=" CA  ILE A 927 "
      ideal   model   delta    sigma   weight residual
     122.26  118.71    3.55 1.24e+00 6.50e-01 8.22e+00
  ... (remaining 18651 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 6997
       17.77 -    35.55: 691
       35.55 -    53.32: 230
       53.32 -    71.10: 137
       71.10 -    88.87: 37
  Dihedral angle restraints: 8092
    sinusoidal: 4648
      harmonic: 3444
  Sorted by residual:
  dihedral pdb=" CA  ILE A 759 "
           pdb=" C   ILE A 759 "
           pdb=" N   VAL A 760 "
           pdb=" CA  VAL A 760 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  123.94   56.06     0      5.00e+00 4.00e-02 1.26e+02
  dihedral pdb=" CA  VAL A 760 "
           pdb=" C   VAL A 760 "
           pdb=" N   ILE A 761 "
           pdb=" CA  ILE A 761 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.17  -32.83     0      5.00e+00 4.00e-02 4.31e+01
  dihedral pdb=" CA  ARG A 765 "
           pdb=" C   ARG A 765 "
           pdb=" N   GLU A 766 "
           pdb=" CA  GLU A 766 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.29   23.71     0      5.00e+00 4.00e-02 2.25e+01
  ... (remaining 8089 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1983
       0.063 -    0.127: 150
       0.127 -    0.190: 7
       0.190 -    0.254: 0
       0.254 -    0.317: 1
  Chirality restraints: 2141
  Sorted by residual:
  chirality pdb=" CB  VAL A 760 "
            pdb=" CA  VAL A 760 "
            pdb=" CG1 VAL A 760 "
            pdb=" CG2 VAL A 760 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.51e+00
  chirality pdb=" C1'   A D  36 "
            pdb=" O4'   A D  36 "
            pdb=" C2'   A D  36 "
            pdb=" N9    A D  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.29    0.17 2.00e-01 2.50e+01 6.97e-01
  chirality pdb=" CA  GLU A 779 "
            pdb=" N   GLU A 779 "
            pdb=" C   GLU A 779 "
            pdb=" CB  GLU A 779 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.36e-01
  ... (remaining 2138 not shown)

  Planarity restraints: 1834
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 759 "   -0.013 2.00e-02 2.50e+03   2.63e-02 6.94e+00
        pdb=" C   ILE A 759 "    0.046 2.00e-02 2.50e+03
        pdb=" O   ILE A 759 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   VAL A 760 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 755 "   -0.031 5.00e-02 4.00e+02   4.77e-02 3.64e+00
        pdb=" N   PRO A 756 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A 756 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 756 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  36 "    0.023 2.00e-02 2.50e+03   1.09e-02 3.25e+00
        pdb=" N9    A D  36 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8    A D  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A D  36 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A D  36 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A D  36 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A D  36 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    A D  36 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  36 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    A D  36 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1831 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 8
        2.02 -     2.74: 1089
        2.74 -     3.46: 18638
        3.46 -     4.18: 32940
        4.18 -     4.90: 51859
  Nonbonded interactions: 104534
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 742 "
            pdb=" OP1   C D  69 "
     model   vdw
     1.297 3.120
  nonbonded pdb=" NH2 ARG A1333 "
            pdb=" O6   DG C   3 "
     model   vdw
     1.298 3.120
  nonbonded pdb=" NE2 GLN A1221 "
            pdb=" OP1  DG C   3 "
     model   vdw
     1.298 3.120
  nonbonded pdb=" NH1 ARG A1335 "
            pdb=" O6   DG C   4 "
     model   vdw
     1.299 3.120
  nonbonded pdb=" NZ  LYS A1340 "
            pdb=" OP2  DA B   8 "
     model   vdw
     1.300 3.120
  ... (remaining 104529 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.28 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:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     17.160
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
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      :  0.003   0.038  13339  Z= 0.125
  Angle     :  0.560   8.616  18656  Z= 0.312
  Chirality :  0.035   0.317   2141
  Planarity :  0.004   0.057   1834
  Dihedral  : 17.572  88.873   5864
  Min Nonbonded Distance : 1.297

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.00 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.38 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.24), residues: 1168
  helix:  1.04 (0.22), residues: 585
  sheet: -0.00 (0.67), residues: 54
  loop : -0.43 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A  71 
 TYR   0.012   0.001   TYR A 594 
 PHE   0.016   0.001   PHE A  86 
 TRP   0.008   0.001   TRP A1126 
 HIS   0.006   0.001   HIS A 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (13339)
  covalent geometry    : angle       0.56022 (18656)
  hydrogen bonds       : bond        0.15504 (  585)
  hydrogen bonds       : angle       5.94761 ( 1568)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 LEU cc_start: 0.9031 (tp) cc_final: 0.8553 (tt)
REVERT: A  399 LEU cc_start: 0.8303 (mt) cc_final: 0.7877 (mt)
REVERT: A  703 THR cc_start: 0.8046 (p) cc_final: 0.7163 (p)
REVERT: A  707 ASP cc_start: 0.9383 (m-30) cc_final: 0.9100 (m-30)
REVERT: A 1350 GLN cc_start: 0.8425 (mm110) cc_final: 0.8075 (mm110)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1516
  time to fit residues: 36.5595
Evaluate side-chains
  100 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:   30.0000
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:   10.0000
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 413 GLN
** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 980 ASN
A 990 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.067180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.054826 restraints weight = 260153.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.057031 restraints weight = 115176.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.058384 restraints weight = 68651.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.059248 restraints weight = 48090.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.059824 restraints weight = 37461.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3166
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3166
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  13339  Z= 0.194
  Angle     :  0.630   8.178  18656  Z= 0.345
  Chirality :  0.039   0.259   2141
  Planarity :  0.005   0.053   1834
  Dihedral  : 18.598  79.221   3349
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.61 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.42 %
    Favored  : 98.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.24), residues: 1168
  helix:  0.70 (0.21), residues: 607
  sheet: -0.33 (0.71), residues: 54
  loop : -0.63 (0.26), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  63 
 TYR   0.014   0.002   TYR A 155 
 PHE   0.018   0.002   PHE A 626 
 TRP   0.008   0.001   TRP A1126 
 HIS   0.007   0.002   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (13339)
  covalent geometry    : angle       0.63005 (18656)
  hydrogen bonds       : bond        0.05249 (  585)
  hydrogen bonds       : angle       4.73555 ( 1568)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 LEU cc_start: 0.9863 (mp) cc_final: 0.9278 (mt)
REVERT: A  161 MET cc_start: 0.9273 (ttt) cc_final: 0.8963 (mtt)
REVERT: A  495 MET cc_start: 0.9579 (mpp) cc_final: 0.9245 (mpp)
REVERT: A  534 MET cc_start: 0.5440 (ptm) cc_final: 0.4621 (ppp)
REVERT: A  631 MET cc_start: 0.9413 (mmp) cc_final: 0.9200 (mmm)
REVERT: A  707 ASP cc_start: 0.9617 (m-30) cc_final: 0.9368 (m-30)
REVERT: A  739 GLN cc_start: 0.9715 (mm-40) cc_final: 0.9313 (mm-40)
REVERT: A  751 MET cc_start: 0.9273 (tpp) cc_final: 0.8850 (tmm)
REVERT: A  936 ASP cc_start: 0.9600 (m-30) cc_final: 0.9337 (m-30)
REVERT: A  943 TYR cc_start: 0.8727 (m-80) cc_final: 0.8516 (m-80)
REVERT: A  981 TYR cc_start: 0.8822 (m-10) cc_final: 0.8247 (m-80)
REVERT: A 1089 MET cc_start: 0.8961 (mpp) cc_final: 0.8679 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1424
  time to fit residues: 21.9712
Evaluate side-chains
  81 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 71 optimal weight:   30.0000
   chunk 79 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 0 optimal weight:   30.0000
   chunk 52 optimal weight:    8.9990
   chunk 87 optimal weight:   20.0000
   chunk 72 optimal weight:    7.9990
   chunk 117 optimal weight:   10.0000
   chunk 35 optimal weight:    7.9990
   chunk 41 optimal weight:    9.9990
   overall best weight:    8.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 612 ASN
A 774 GLN
A 776 ASN
** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 869 ASN
** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1256 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.058757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.048103 restraints weight = 175454.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.049672 restraints weight = 93059.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.050647 restraints weight = 61479.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.051267 restraints weight = 46172.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.051679 restraints weight = 37882.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.4982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  13339  Z= 0.270
  Angle     :  0.738  12.431  18656  Z= 0.398
  Chirality :  0.042   0.266   2141
  Planarity :  0.006   0.072   1834
  Dihedral  : 19.305  81.146   3349
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 23.77
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.78 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.89 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.23), residues: 1168
  helix: -0.12 (0.20), residues: 615
  sheet:  0.92 (0.81), residues: 42
  loop : -0.98 (0.25), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 324 
 TYR   0.027   0.003   TYR A1294 
 PHE   0.022   0.003   PHE A 446 
 TRP   0.017   0.002   TRP A 464 
 HIS   0.010   0.002   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 (13339)
  covalent geometry    : angle       0.73821 (18656)
  hydrogen bonds       : bond        0.06257 (  585)
  hydrogen bonds       : angle       5.05482 ( 1568)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.495 
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  158 LEU cc_start: 0.9874 (mp) cc_final: 0.9630 (mt)
REVERT: A  161 MET cc_start: 0.9534 (ttt) cc_final: 0.9248 (mtp)
REVERT: A  294 LYS cc_start: 0.6636 (pttm) cc_final: 0.6147 (tmtt)
REVERT: A  321 MET cc_start: 0.9160 (mmp) cc_final: 0.8817 (mmp)
REVERT: A  495 MET cc_start: 0.9401 (mpp) cc_final: 0.9005 (mpp)
REVERT: A  534 MET cc_start: 0.4105 (ptm) cc_final: 0.3482 (ppp)
REVERT: A  587 PHE cc_start: 0.8590 (m-80) cc_final: 0.7286 (m-80)
REVERT: A  631 MET cc_start: 0.9393 (mmp) cc_final: 0.9124 (mmm)
REVERT: A  707 ASP cc_start: 0.9730 (m-30) cc_final: 0.9506 (m-30)
REVERT: A  739 GLN cc_start: 0.9691 (mm-40) cc_final: 0.9343 (mm-40)
REVERT: A  936 ASP cc_start: 0.9238 (m-30) cc_final: 0.8904 (m-30)
REVERT: A  939 MET cc_start: 0.8267 (tmm) cc_final: 0.7977 (tmm)
REVERT: A  981 TYR cc_start: 0.9100 (m-80) cc_final: 0.8450 (m-80)
REVERT: A 1089 MET cc_start: 0.9194 (mpp) cc_final: 0.8659 (mpp)
REVERT: A 1097 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8755 (tmtt)
REVERT: A 1169 MET cc_start: 0.8296 (tpt) cc_final: 0.7661 (tpt)
REVERT: A 1201 TYR cc_start: 0.9492 (m-80) cc_final: 0.8962 (m-80)
REVERT: A 1214 LEU cc_start: 0.9708 (mt) cc_final: 0.9267 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1364
  time to fit residues: 18.0653
Evaluate side-chains
  64 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 1 optimal weight:   40.0000
   chunk 47 optimal weight:   10.0000
   chunk 0 optimal weight:   30.0000
   chunk 15 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   chunk 103 optimal weight:   30.0000
   chunk 89 optimal weight:    8.9990
   chunk 69 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1093 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.057868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.047112 restraints weight = 199453.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.048790 restraints weight = 100152.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.049838 restraints weight = 63709.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.050501 restraints weight = 46978.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.050935 restraints weight = 37907.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3002
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.5794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  13339  Z= 0.232
  Angle     :  0.649   8.555  18656  Z= 0.355
  Chirality :  0.040   0.287   2141
  Planarity :  0.004   0.055   1834
  Dihedral  : 19.161  81.191   3349
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 20.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.86 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.42 %
    Favored  : 98.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.23), residues: 1168
  helix: -0.14 (0.20), residues: 611
  sheet: -0.96 (0.84), residues: 37
  loop : -0.98 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 778 
 TYR   0.017   0.002   TYR A1294 
 PHE   0.018   0.002   PHE A 972 
 TRP   0.016   0.002   TRP A 464 
 HIS   0.011   0.002   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (13339)
  covalent geometry    : angle       0.64926 (18656)
  hydrogen bonds       : bond        0.05584 (  585)
  hydrogen bonds       : angle       4.88013 ( 1568)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ASP cc_start: 0.8839 (p0) cc_final: 0.8636 (p0)
REVERT: A  158 LEU cc_start: 0.9880 (mp) cc_final: 0.9662 (mt)
REVERT: A  161 MET cc_start: 0.9550 (ttt) cc_final: 0.9278 (mtp)
REVERT: A  294 LYS cc_start: 0.6733 (pttm) cc_final: 0.6057 (tmtt)
REVERT: A  321 MET cc_start: 0.9195 (mmp) cc_final: 0.8786 (mmp)
REVERT: A  383 MET cc_start: 0.7369 (tpt) cc_final: 0.6759 (tpt)
REVERT: A  495 MET cc_start: 0.9420 (mpp) cc_final: 0.9036 (mpp)
REVERT: A  534 MET cc_start: 0.5137 (ptm) cc_final: 0.4499 (ppp)
REVERT: A  564 LEU cc_start: 0.9356 (mm) cc_final: 0.9110 (mm)
REVERT: A  587 PHE cc_start: 0.8778 (m-80) cc_final: 0.7805 (m-80)
REVERT: A  707 ASP cc_start: 0.9704 (m-30) cc_final: 0.9406 (m-30)
REVERT: A  739 GLN cc_start: 0.9673 (mm-40) cc_final: 0.9362 (mm-40)
REVERT: A  939 MET cc_start: 0.8445 (tmm) cc_final: 0.8122 (tmm)
REVERT: A  981 TYR cc_start: 0.9208 (m-80) cc_final: 0.8502 (m-80)
REVERT: A 1089 MET cc_start: 0.9184 (mpp) cc_final: 0.8859 (mpp)
REVERT: A 1169 MET cc_start: 0.8323 (tpt) cc_final: 0.8023 (tpt)
REVERT: A 1201 TYR cc_start: 0.9479 (m-80) cc_final: 0.9052 (m-80)
REVERT: A 1214 LEU cc_start: 0.9720 (mt) cc_final: 0.9348 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1230
  time to fit residues: 15.0111
Evaluate side-chains
  62 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 91 optimal weight:    7.9990
   chunk 95 optimal weight:   20.0000
   chunk 104 optimal weight:   20.0000
   chunk 39 optimal weight:    8.9990
   chunk 80 optimal weight:   20.0000
   chunk 64 optimal weight:   30.0000
   chunk 12 optimal weight:    5.9990
   chunk 102 optimal weight:    9.9990
   chunk 73 optimal weight:   10.0000
   chunk 117 optimal weight:   10.0000
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.042609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.030466 restraints weight = 172533.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.031639 restraints weight = 105218.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.032423 restraints weight = 76148.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.032939 restraints weight = 61056.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.033337 restraints weight = 52538.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.6806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  13339  Z= 0.228
  Angle     :  0.660   8.482  18656  Z= 0.356
  Chirality :  0.040   0.239   2141
  Planarity :  0.005   0.060   1834
  Dihedral  : 19.475  81.243   3349
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 21.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.95 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.42 %
    Favored  : 98.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.23), residues: 1168
  helix: -0.17 (0.20), residues: 611
  sheet: -0.91 (0.81), residues: 37
  loop : -0.94 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  63 
 TYR   0.018   0.002   TYR A1294 
 PHE   0.020   0.002   PHE A 446 
 TRP   0.020   0.002   TRP A 464 
 HIS   0.011   0.002   HIS A 930 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (13339)
  covalent geometry    : angle       0.66026 (18656)
  hydrogen bonds       : bond        0.05794 (  585)
  hydrogen bonds       : angle       4.94457 ( 1568)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.461 
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   39 ASP cc_start: 0.8710 (p0) cc_final: 0.8501 (p0)
REVERT: A  161 MET cc_start: 0.9518 (ttt) cc_final: 0.9250 (mtp)
REVERT: A  321 MET cc_start: 0.9280 (mmp) cc_final: 0.8793 (mmp)
REVERT: A  495 MET cc_start: 0.9452 (mpp) cc_final: 0.9070 (mpp)
REVERT: A  564 LEU cc_start: 0.9349 (mm) cc_final: 0.9145 (mm)
REVERT: A  587 PHE cc_start: 0.8641 (m-80) cc_final: 0.7682 (m-80)
REVERT: A  629 ARG cc_start: 0.9653 (ppt170) cc_final: 0.9383 (ptm-80)
REVERT: A  707 ASP cc_start: 0.9709 (m-30) cc_final: 0.9443 (m-30)
REVERT: A  739 GLN cc_start: 0.9645 (mm-40) cc_final: 0.9358 (mm-40)
REVERT: A  986 ASP cc_start: 0.8695 (m-30) cc_final: 0.8483 (t0)
REVERT: A 1089 MET cc_start: 0.9274 (mpp) cc_final: 0.8870 (mpp)
REVERT: A 1169 MET cc_start: 0.8529 (tpt) cc_final: 0.8271 (tpt)
REVERT: A 1201 TYR cc_start: 0.9496 (m-80) cc_final: 0.9279 (m-80)
REVERT: A 1214 LEU cc_start: 0.9659 (mt) cc_final: 0.9141 (tt)
REVERT: A 1315 LEU cc_start: 0.9566 (tp) cc_final: 0.9351 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1261
  time to fit residues: 15.4708
Evaluate side-chains
  60 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 111 optimal weight:   20.0000
   chunk 29 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 85 optimal weight:    5.9990
   chunk 80 optimal weight:   20.0000
   chunk 110 optimal weight:    4.9990
   chunk 77 optimal weight:   20.0000
   chunk 34 optimal weight:    6.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 723 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.045631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.032790 restraints weight = 172199.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.034176 restraints weight = 100333.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.034974 restraints weight = 70389.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.035637 restraints weight = 56298.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.036089 restraints weight = 47569.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.6872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13339  Z= 0.135
  Angle     :  0.547   6.671  18656  Z= 0.300
  Chirality :  0.036   0.202   2141
  Planarity :  0.003   0.037   1834
  Dihedral  : 19.065  81.663   3349
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.26 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.23 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.24), residues: 1168
  helix:  0.30 (0.21), residues: 614
  sheet: -1.12 (0.63), residues: 59
  loop : -0.79 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  63 
 TYR   0.015   0.001   TYR A 155 
 PHE   0.020   0.001   PHE A 972 
 TRP   0.010   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A 930 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (13339)
  covalent geometry    : angle       0.54715 (18656)
  hydrogen bonds       : bond        0.04811 (  585)
  hydrogen bonds       : angle       4.57859 ( 1568)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ASP cc_start: 0.8811 (p0) cc_final: 0.8605 (p0)
REVERT: A  161 MET cc_start: 0.9501 (ttt) cc_final: 0.9103 (tmm)
REVERT: A  321 MET cc_start: 0.9181 (mmp) cc_final: 0.8710 (mmp)
REVERT: A  495 MET cc_start: 0.9518 (mpp) cc_final: 0.9119 (mpp)
REVERT: A  564 LEU cc_start: 0.9262 (mm) cc_final: 0.9028 (mm)
REVERT: A  587 PHE cc_start: 0.8494 (m-80) cc_final: 0.7605 (m-80)
REVERT: A  629 ARG cc_start: 0.9578 (ppt170) cc_final: 0.9368 (ptm-80)
REVERT: A  707 ASP cc_start: 0.9684 (m-30) cc_final: 0.9404 (m-30)
REVERT: A  739 GLN cc_start: 0.9637 (mm-40) cc_final: 0.9336 (mm-40)
REVERT: A  802 GLU cc_start: 0.9555 (mt-10) cc_final: 0.9262 (mp0)
REVERT: A  939 MET cc_start: 0.8608 (tmm) cc_final: 0.8237 (tmm)
REVERT: A  981 TYR cc_start: 0.9222 (m-80) cc_final: 0.8305 (m-80)
REVERT: A 1089 MET cc_start: 0.9168 (mpp) cc_final: 0.8630 (mpp)
REVERT: A 1201 TYR cc_start: 0.9547 (m-80) cc_final: 0.9180 (m-80)
REVERT: A 1214 LEU cc_start: 0.9621 (mt) cc_final: 0.9188 (tt)
REVERT: A 1315 LEU cc_start: 0.9573 (tp) cc_final: 0.9371 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1210
  time to fit residues: 14.8383
Evaluate side-chains
  63 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 11 optimal weight:    8.9990
   chunk 79 optimal weight:    4.9990
   chunk 123 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   chunk 129 optimal weight:   20.0000
   chunk 53 optimal weight:    3.9990
   chunk 73 optimal weight:   20.0000
   chunk 76 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 117 optimal weight:   10.0000
   chunk 93 optimal weight:    1.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  99 HIS
** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1297 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.043237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.030584 restraints weight = 209956.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.031964 restraints weight = 116861.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.032872 restraints weight = 80441.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.033521 restraints weight = 62303.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.033965 restraints weight = 52146.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.7284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13339  Z= 0.174
  Angle     :  0.577   7.307  18656  Z= 0.312
  Chirality :  0.038   0.355   2141
  Planarity :  0.004   0.042   1834
  Dihedral  : 19.185  80.396   3349
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 17.67
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.61 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.95 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.24), residues: 1168
  helix:  0.30 (0.21), residues: 613
  sheet: -0.68 (0.86), residues: 37
  loop : -0.75 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  71 
 TYR   0.020   0.002   TYR A1294 
 PHE   0.017   0.002   PHE A 972 
 TRP   0.014   0.002   TRP A 464 
 HIS   0.007   0.001   HIS A 930 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (13339)
  covalent geometry    : angle       0.57659 (18656)
  hydrogen bonds       : bond        0.05033 (  585)
  hydrogen bonds       : angle       4.62459 ( 1568)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.9204 (mmp) cc_final: 0.8687 (mmp)
REVERT: A  495 MET cc_start: 0.9517 (mpp) cc_final: 0.9151 (mpp)
REVERT: A  564 LEU cc_start: 0.9296 (mm) cc_final: 0.9080 (mm)
REVERT: A  587 PHE cc_start: 0.8582 (m-80) cc_final: 0.7690 (m-80)
REVERT: A  629 ARG cc_start: 0.9587 (ppt170) cc_final: 0.9325 (ptm-80)
REVERT: A  707 ASP cc_start: 0.9690 (m-30) cc_final: 0.9426 (m-30)
REVERT: A  739 GLN cc_start: 0.9646 (mm-40) cc_final: 0.9361 (mm-40)
REVERT: A  802 GLU cc_start: 0.9539 (mt-10) cc_final: 0.9310 (mp0)
REVERT: A  939 MET cc_start: 0.8695 (tmm) cc_final: 0.8353 (tmm)
REVERT: A  986 ASP cc_start: 0.8686 (m-30) cc_final: 0.8467 (t0)
REVERT: A 1089 MET cc_start: 0.9242 (mpp) cc_final: 0.8867 (mpp)
REVERT: A 1169 MET cc_start: 0.8126 (tpt) cc_final: 0.7555 (tpt)
REVERT: A 1201 TYR cc_start: 0.9532 (m-80) cc_final: 0.9088 (m-80)
REVERT: A 1214 LEU cc_start: 0.9633 (mt) cc_final: 0.9197 (tt)
REVERT: A 1315 LEU cc_start: 0.9567 (tp) cc_final: 0.9345 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1186
  time to fit residues: 13.7799
Evaluate side-chains
  61 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 99 optimal weight:    8.9990
   chunk 44 optimal weight:    9.9990
   chunk 95 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 50 optimal weight:   10.0000
   chunk 71 optimal weight:   20.0000
   chunk 96 optimal weight:   20.0000
   chunk 124 optimal weight:   20.0000
   chunk 2 optimal weight:    0.8980
   chunk 128 optimal weight:   20.0000
   chunk 98 optimal weight:    0.7980
   overall best weight:    4.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.044309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.031423 restraints weight = 232355.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.032927 restraints weight = 119265.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.033932 restraints weight = 79014.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.034625 restraints weight = 59913.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.035109 restraints weight = 49305.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2931
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.7517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13339  Z= 0.154
  Angle     :  0.558   8.913  18656  Z= 0.302
  Chirality :  0.037   0.268   2141
  Planarity :  0.003   0.036   1834
  Dihedral  : 19.135  79.773   3349
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.52 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.19 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.24), residues: 1168
  helix:  0.43 (0.21), residues: 611
  sheet: -0.62 (0.88), residues: 37
  loop : -0.77 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 778 
 TYR   0.015   0.001   TYR A 155 
 PHE   0.015   0.001   PHE A 972 
 TRP   0.013   0.001   TRP A 464 
 HIS   0.010   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (13339)
  covalent geometry    : angle       0.55787 (18656)
  hydrogen bonds       : bond        0.04874 (  585)
  hydrogen bonds       : angle       4.51609 ( 1568)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ARG cc_start: 0.9605 (ttm170) cc_final: 0.9273 (tpm170)
REVERT: A   79 ILE cc_start: 0.9678 (mm) cc_final: 0.9228 (mt)
REVERT: A  321 MET cc_start: 0.9146 (mmp) cc_final: 0.8627 (mmp)
REVERT: A  495 MET cc_start: 0.9527 (mpp) cc_final: 0.9154 (mpp)
REVERT: A  564 LEU cc_start: 0.9393 (mm) cc_final: 0.9148 (mm)
REVERT: A  587 PHE cc_start: 0.8560 (m-80) cc_final: 0.7676 (m-80)
REVERT: A  629 ARG cc_start: 0.9576 (ppt170) cc_final: 0.9330 (ptm-80)
REVERT: A  739 GLN cc_start: 0.9634 (mm-40) cc_final: 0.9359 (mm-40)
REVERT: A  802 GLU cc_start: 0.9575 (mt-10) cc_final: 0.9290 (mp0)
REVERT: A  939 MET cc_start: 0.8667 (tmm) cc_final: 0.8309 (tmm)
REVERT: A 1089 MET cc_start: 0.9249 (mpp) cc_final: 0.8873 (mpp)
REVERT: A 1169 MET cc_start: 0.8206 (tpt) cc_final: 0.7672 (tpt)
REVERT: A 1201 TYR cc_start: 0.9535 (m-80) cc_final: 0.9109 (m-80)
REVERT: A 1214 LEU cc_start: 0.9645 (mt) cc_final: 0.9230 (tt)
REVERT: A 1315 LEU cc_start: 0.9569 (tp) cc_final: 0.9338 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1233
  time to fit residues: 14.2203
Evaluate side-chains
  65 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 20 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0010
   chunk 119 optimal weight:   10.0000
   chunk 124 optimal weight:   20.0000
   chunk 123 optimal weight:   20.0000
   chunk 24 optimal weight:   20.0000
   chunk 86 optimal weight:    6.9990
   chunk 64 optimal weight:   50.0000
   chunk 59 optimal weight:    0.7980
   overall best weight:    4.9592

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 GLN
A 894 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.042931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.030160 restraints weight = 237526.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.031628 restraints weight = 124236.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.032633 restraints weight = 83013.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.033323 restraints weight = 63030.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.033790 restraints weight = 51962.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.7774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13339  Z= 0.166
  Angle     :  0.566   7.044  18656  Z= 0.307
  Chirality :  0.037   0.367   2141
  Planarity :  0.004   0.039   1834
  Dihedral  : 19.180  81.630   3349
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 16.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.95 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.28 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.24), residues: 1168
  helix:  0.41 (0.21), residues: 612
  sheet: -0.65 (0.88), residues: 37
  loop : -0.79 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  71 
 TYR   0.011   0.001   TYR A 155 
 PHE   0.015   0.002   PHE A 972 
 TRP   0.014   0.002   TRP A 464 
 HIS   0.008   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (13339)
  covalent geometry    : angle       0.56623 (18656)
  hydrogen bonds       : bond        0.05012 (  585)
  hydrogen bonds       : angle       4.55464 ( 1568)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.453 
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  161 MET cc_start: 0.9448 (mtm) cc_final: 0.9156 (ptp)
REVERT: A  321 MET cc_start: 0.9136 (mmp) cc_final: 0.8584 (mmp)
REVERT: A  495 MET cc_start: 0.9520 (mpp) cc_final: 0.9170 (mpp)
REVERT: A  587 PHE cc_start: 0.8564 (m-80) cc_final: 0.7778 (m-80)
REVERT: A  629 ARG cc_start: 0.9570 (ppt170) cc_final: 0.9294 (ptm-80)
REVERT: A  739 GLN cc_start: 0.9646 (mm-40) cc_final: 0.9352 (mm-40)
REVERT: A  802 GLU cc_start: 0.9550 (mt-10) cc_final: 0.9321 (mp0)
REVERT: A  879 MET cc_start: 0.8817 (tpp) cc_final: 0.7978 (tpp)
REVERT: A  939 MET cc_start: 0.8639 (tmm) cc_final: 0.8310 (tmm)
REVERT: A 1089 MET cc_start: 0.9260 (mpp) cc_final: 0.8875 (mpp)
REVERT: A 1169 MET cc_start: 0.8224 (tpt) cc_final: 0.7669 (tpt)
REVERT: A 1201 TYR cc_start: 0.9527 (m-80) cc_final: 0.9079 (m-80)
REVERT: A 1214 LEU cc_start: 0.9654 (mt) cc_final: 0.9250 (tt)
REVERT: A 1315 LEU cc_start: 0.9522 (tp) cc_final: 0.9272 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1321
  time to fit residues: 14.9605
Evaluate side-chains
  61 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 9 optimal weight:   20.0000
   chunk 87 optimal weight:    5.9990
   chunk 89 optimal weight:    0.3980
   chunk 78 optimal weight:    0.3980
   chunk 13 optimal weight:    7.9990
   chunk 73 optimal weight:   20.0000
   chunk 58 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 12 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 GLN
** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.046532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.033138 restraints weight = 200673.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.034721 restraints weight = 106629.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.035798 restraints weight = 71351.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.036498 restraints weight = 54344.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.037002 restraints weight = 45082.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2994
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2994
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.7732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13339  Z= 0.110
  Angle     :  0.538   8.577  18656  Z= 0.288
  Chirality :  0.037   0.361   2141
  Planarity :  0.003   0.034   1834
  Dihedral  : 18.806  81.129   3349
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.00 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.09 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.25), residues: 1168
  helix:  0.77 (0.21), residues: 615
  sheet: -1.02 (0.63), residues: 66
  loop : -0.58 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  71 
 TYR   0.016   0.001   TYR A 155 
 PHE   0.011   0.001   PHE A  86 
 TRP   0.010   0.001   TRP A  18 
 HIS   0.005   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (13339)
  covalent geometry    : angle       0.53787 (18656)
  hydrogen bonds       : bond        0.04706 (  585)
  hydrogen bonds       : angle       4.20018 ( 1568)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.420 
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  161 MET cc_start: 0.9469 (mtm) cc_final: 0.9195 (ptp)
REVERT: A  321 MET cc_start: 0.9088 (mmp) cc_final: 0.8645 (mmp)
REVERT: A  495 MET cc_start: 0.9527 (mpp) cc_final: 0.9187 (mpp)
REVERT: A  564 LEU cc_start: 0.9358 (mm) cc_final: 0.9100 (mm)
REVERT: A  587 PHE cc_start: 0.8269 (m-80) cc_final: 0.7358 (m-80)
REVERT: A  629 ARG cc_start: 0.9547 (ppt170) cc_final: 0.9330 (ptm-80)
REVERT: A  852 ILE cc_start: 0.9493 (pt) cc_final: 0.9182 (mm)
REVERT: A  939 MET cc_start: 0.8517 (tmm) cc_final: 0.8147 (tmm)
REVERT: A 1089 MET cc_start: 0.9100 (mpp) cc_final: 0.8797 (mpp)
REVERT: A 1169 MET cc_start: 0.8216 (tpt) cc_final: 0.7754 (tpt)
REVERT: A 1201 TYR cc_start: 0.9532 (m-80) cc_final: 0.9259 (m-80)
REVERT: A 1214 LEU cc_start: 0.9596 (mt) cc_final: 0.9249 (pp)
REVERT: A 1226 LEU cc_start: 0.9426 (tt) cc_final: 0.8960 (mp)
REVERT: A 1315 LEU cc_start: 0.9538 (tp) cc_final: 0.9167 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.1161
  time to fit residues: 15.4992
Evaluate side-chains
  67 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 124 optimal weight:   20.0000
   chunk 77 optimal weight:   10.0000
   chunk 129 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   chunk 18 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0070
   chunk 55 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 113 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   overall best weight:    5.2006

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 GLN
** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.044179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.032108 restraints weight = 206142.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.033554 restraints weight = 109412.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.034530 restraints weight = 73153.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.035167 restraints weight = 55850.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.035605 restraints weight = 46450.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2939
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2939 r_free = 0.2939    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2939 r_free = 0.2939    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2939
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.7954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13339  Z= 0.172
  Angle     :  0.573   8.084  18656  Z= 0.310
  Chirality :  0.037   0.299   2141
  Planarity :  0.004   0.046   1834
  Dihedral  : 18.998  83.429   3349
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.43 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.19 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.24), residues: 1168
  helix:  0.65 (0.21), residues: 613
  sheet: -0.62 (0.86), residues: 38
  loop : -0.74 (0.26), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  71 
 TYR   0.011   0.002   TYR A 132 
 PHE   0.014   0.002   PHE A 446 
 TRP   0.014   0.002   TRP A 464 
 HIS   0.009   0.002   HIS A 930 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (13339)
  covalent geometry    : angle       0.57305 (18656)
  hydrogen bonds       : bond        0.05006 (  585)
  hydrogen bonds       : angle       4.48180 ( 1568)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2624.05 seconds
wall clock time: 46 minutes 14.90 seconds (2774.90 seconds total)