Starting phenix.real_space_refine
on Wed Feb  4 14:46:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w7t_65732/02_2026/9w7t_65732.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w7t_65732/02_2026/9w7t_65732.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w7t_65732/02_2026/9w7t_65732.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w7t_65732/02_2026/9w7t_65732.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w7t_65732/02_2026/9w7t_65732.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w7t_65732/02_2026/9w7t_65732.map"
  }
  resolution = 3.91
  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=   0.005 sd=   0.045
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     144      5.49       5
     S      19      5.16       5
     C    6614      2.51       5
     N    1982      2.21       5
     O    2475      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  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: 11234
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 993, 8142
          Classifications: {'peptide': 993}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 966}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 698
          Classifications: {'DNA': 34}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 33}
    Chain: "C"
      Number of atoms: 305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 305
          Classifications: {'DNA': 15}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 14}
    Chain: "D"
      Number of atoms: 2089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2089
          Classifications: {'RNA': 98}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 48, 'rna3p_pyr': 38}
          Link IDs: {'rna2p': 11, 'rna3p': 86}
  Time building chain proxies: 2.70, per 1000 atoms: 0.24
  Number of scatterers: 11234
  At special positions: 0
  Unit cell: (120.736, 102.41, 140.14, 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      19     16.00
     P     144     15.00
     O    2475      8.00
     N    1982      7.00
     C    6614      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: 1.02
  Conformation dependent library (CDL) restraints added in 437.8 milliseconds
  

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1886

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 8 sheets defined
      54.2% alpha, 10.2% beta
      49 base pairs and 87 stacking pairs defined.
    Time for finding SS restraints: 1.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 4.712A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 104 through 106
      No H-bonds generated for 'chain 'A' and resid 104 through 106'
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.581A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.637A  pdb=" N   PHE A 164 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
    Processing helix  chain 'A' and resid 346 through 353
      removed outlier: 3.543A  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 382
      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: 3.614A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.277A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.935A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASP A 435 " --> pdb=" O   PRO A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 483 through 495
      removed outlier: 4.196A  pdb=" N   MET A 495 " --> pdb=" O   PHE A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 4.092A  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 560 through 568
    Processing helix  chain 'A' and resid 591 through 601
    Processing helix  chain 'A' and resid 603 through 608
      removed outlier: 3.538A  pdb=" N   LEU A 607 " --> pdb=" O   ASP A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 611
      No H-bonds generated for 'chain 'A' and resid 609 through 611'
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 643
      removed outlier: 4.599A  pdb=" N   HIS A 641 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 652
    Processing helix  chain 'A' and resid 664 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 702 through 711
      removed outlier: 4.338A  pdb=" N   GLU A 706 " --> pdb=" O   LEU A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 726
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 3.532A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 927 through 940
    Processing helix  chain 'A' and resid 959 through 971
      removed outlier: 4.090A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 999
      removed outlier: 4.423A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1088
    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 1185
      removed outlier: 3.513A  pdb=" N   LYS A1185 " --> pdb=" O   PHE A1181 " (cutoff:3.500A)
    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
      removed outlier: 3.551A  pdb=" N   HIS A1262 " --> pdb=" O   PHE A1258 " (cutoff:3.500A)
    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 1313
      removed outlier: 3.657A  pdb=" N   HIS A1311 " --> pdb=" O   GLU A1307 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   PHE A1313 " --> pdb=" O   ILE A1309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1314 through 1316
      No H-bonds generated for 'chain 'A' and resid 1314 through 1316'
    Processing helix  chain 'A' and resid 1340 through 1344
      removed outlier: 3.681A  pdb=" N   ASP A1344 " --> pdb=" O   GLU A1341 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957
      removed outlier: 6.479A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   TYR A   5 " --> pdb=" O   ASN A 758 " (cutoff:3.500A)
      removed outlier: 8.741A  pdb=" N   VAL A 760 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   GLU A 762 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   LEU A   9 " --> pdb=" O   GLU A 762 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33
    Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36
      removed outlier: 6.606A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 8.260A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 509
      removed outlier: 5.428A  pdb=" N   LEU A 508 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 539
      removed outlier: 3.510A  pdb=" N   TYR A 529 " --> pdb=" O   ALA A 538 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LYS A 528 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1106 through 1111
      removed outlier: 6.692A  pdb=" N   LYS A1107 " --> pdb=" O   PRO A1137 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   SER A1109 " --> pdb=" O   ASP A1135 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   ASP A1135 " --> pdb=" O   SER A1109 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY A1133 " --> pdb=" O   LEU A1111 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.532A  pdb=" N   LYS A1156 " --> pdb=" O   LYS A1151 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU A1164 " --> pdb=" O   VAL A1143 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1326

    379 hydrogen bonds defined for protein.
    1095 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      124 hydrogen bonds
      236 hydrogen bond angles
      0 basepair planarities
      49 basepair parallelities
      87 stacking parallelities
  Total time for adding SS restraints: 2.72

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2703
        1.33 -     1.45: 2946
        1.45 -     1.57: 5783
        1.57 -     1.69: 288
        1.69 -     1.81: 36
  Bond restraints: 11756
  Sorted by residual:
  bond pdb=" C3'  DG B   7 "
       pdb=" O3'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.41e+00
  bond pdb=" CA  ASP A  94 "
       pdb=" C   ASP A  94 "
    ideal  model  delta    sigma   weight residual
    1.522  1.533 -0.011 1.08e-02 8.57e+03 1.02e+00
  bond pdb=" C3'  DA B   8 "
       pdb=" C2'  DA B   8 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.00e-02 2.50e+03 8.07e-01
  bond pdb=" C3'  DC C   8 "
       pdb=" C2'  DC C   8 "
    ideal  model  delta    sigma   weight residual
    1.525  1.542 -0.017 2.00e-02 2.50e+03 7.10e-01
  bond pdb=" C3'  DG B   7 "
       pdb=" C2'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.525  1.542 -0.017 2.00e-02 2.50e+03 6.97e-01
  ... (remaining 11751 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.95: 15620
        0.95 -     1.90: 745
        1.90 -     2.85: 124
        2.85 -     3.80: 17
        3.80 -     4.75: 3
  Bond angle restraints: 16509
  Sorted by residual:
  angle pdb=" C   GLU A 480 "
        pdb=" N   VAL A 481 "
        pdb=" CA  VAL A 481 "
      ideal   model   delta    sigma   weight residual
     122.66  120.43    2.23 9.70e-01 1.06e+00 5.31e+00
  angle pdb=" C   TYR A 362 "
        pdb=" N   ILE A 363 "
        pdb=" CA  ILE A 363 "
      ideal   model   delta    sigma   weight residual
     122.97  120.88    2.09 9.80e-01 1.04e+00 4.54e+00
  angle pdb=" C   PHE A 164 "
        pdb=" N   ARG A 165 "
        pdb=" CA  ARG A 165 "
      ideal   model   delta    sigma   weight residual
     120.60  124.00   -3.40 1.60e+00 3.91e-01 4.52e+00
  angle pdb=" N   LYS A 468 "
        pdb=" CA  LYS A 468 "
        pdb=" C   LYS A 468 "
      ideal   model   delta    sigma   weight residual
     111.14  113.26   -2.12 1.08e+00 8.57e-01 3.85e+00
  angle pdb=" N   LEU A 551 "
        pdb=" CA  LEU A 551 "
        pdb=" C   LEU A 551 "
      ideal   model   delta    sigma   weight residual
     111.36  113.50   -2.14 1.09e+00 8.42e-01 3.85e+00
  ... (remaining 16504 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.59: 6755
       34.59 -    69.17: 317
       69.17 -   103.75: 26
      103.75 -   138.34: 0
      138.34 -   172.92: 1
  Dihedral angle restraints: 7099
    sinusoidal: 4184
      harmonic: 2915
  Sorted by residual:
  dihedral pdb=" C4'  DG B   7 "
           pdb=" C3'  DG B   7 "
           pdb=" O3'  DG B   7 "
           pdb=" P    DA B   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   47.08  172.92     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" CA  PHE A 446 "
           pdb=" C   PHE A 446 "
           pdb=" N   ARG A 447 "
           pdb=" CA  ARG A 447 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.59   16.41     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CG  ARG A1359 "
           pdb=" CD  ARG A1359 "
           pdb=" NE  ARG A1359 "
           pdb=" CZ  ARG A1359 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.83  -43.17     2      1.50e+01 4.44e-03 9.99e+00
  ... (remaining 7096 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1300
       0.026 -    0.052: 381
       0.052 -    0.078: 140
       0.078 -    0.104: 55
       0.104 -    0.130: 28
  Chirality restraints: 1904
  Sorted by residual:
  chirality pdb=" C1'   A D  74 "
            pdb=" O4'   A D  74 "
            pdb=" C2'   A D  74 "
            pdb=" N9    A D  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.33    0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" C1'   A D  34 "
            pdb=" O4'   A D  34 "
            pdb=" C2'   A D  34 "
            pdb=" N9    A D  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.33    0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  ILE A 956 "
            pdb=" N   ILE A 956 "
            pdb=" C   ILE A 956 "
            pdb=" CB  ILE A 956 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.14e-01
  ... (remaining 1901 not shown)

  Planarity restraints: 1565
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  74 "   -0.023 2.00e-02 2.50e+03   1.03e-02 2.92e+00
        pdb=" N9    A D  74 "    0.024 2.00e-02 2.50e+03
        pdb=" C8    A D  74 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A D  74 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A D  74 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A D  74 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A D  74 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A D  74 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  74 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  74 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A D  74 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1228 "   -0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO A1229 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A1229 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A1229 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  34 "    0.019 2.00e-02 2.50e+03   8.76e-03 2.11e+00
        pdb=" N9    A D  34 "   -0.021 2.00e-02 2.50e+03
        pdb=" C8    A D  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A D  34 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A D  34 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A D  34 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A D  34 "    0.004 2.00e-02 2.50e+03
        pdb=" N1    A D  34 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A D  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  34 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  34 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1562 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 4
        2.02 -     2.74: 885
        2.74 -     3.46: 15375
        3.46 -     4.18: 28452
        4.18 -     4.90: 45448
  Nonbonded interactions: 90164
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A  44 "
            pdb=" O6    G D  92 "
     model   vdw
     1.297 3.120
  nonbonded pdb=" ND2 ASN A  77 "
            pdb=" O2    U D  59 "
     model   vdw
     1.297 3.120
  nonbonded pdb=" NH2 ARG A1122 "
            pdb=" N3    A D  49 "
     model   vdw
     1.353 3.200
  nonbonded pdb=" NH1 ARG A  71 "
            pdb=" C5    C D  18 "
     model   vdw
     1.431 3.420
  nonbonded pdb=" N2   DG B   7 "
            pdb=" O2   DC C  10 "
     model   vdw
     2.101 2.496
  ... (remaining 90159 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.670
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.500
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
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      :  0.002   0.036  11756  Z= 0.115
  Angle     :  0.466   4.754  16509  Z= 0.280
  Chirality :  0.033   0.130   1904
  Planarity :  0.003   0.042   1565
  Dihedral  : 16.781 172.925   5213
  Min Nonbonded Distance : 1.297

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.27), residues: 985
  helix:  2.09 (0.24), residues: 480
  sheet:  1.53 (0.58), residues: 83
  loop :  0.18 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1122 
 TYR   0.008   0.001   TYR A 517 
 PHE   0.013   0.001   PHE A 432 
 TRP   0.011   0.001   TRP A1126 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 (11756)
  covalent geometry    : angle       0.46606 (16509)
  hydrogen bonds       : bond        0.15070 (  503)
  hydrogen bonds       : angle       5.09930 ( 1331)

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  473 ILE cc_start: 0.9129 (mt) cc_final: 0.8926 (tp)
REVERT: A  534 MET cc_start: 0.5461 (mtt) cc_final: 0.4391 (ttm)
REVERT: A  562 LYS cc_start: 0.9266 (tttt) cc_final: 0.8937 (tppt)
REVERT: A  585 ASP cc_start: 0.8275 (m-30) cc_final: 0.7950 (m-30)
REVERT: A  586 ARG cc_start: 0.9323 (ptp-170) cc_final: 0.9041 (ppt170)
REVERT: A  969 ASP cc_start: 0.9101 (m-30) cc_final: 0.8363 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1353
  time to fit residues: 37.5091
Evaluate side-chains
  126 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0030
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:   20.0000
   overall best weight:    3.1998

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

Flipped N/Q/H residues before XYZ refinement:
A 341 GLN
** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 563 GLN
** A 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 980 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.044425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.032928 restraints weight = 81085.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.034262 restraints weight = 39806.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.035194 restraints weight = 25478.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.035829 restraints weight = 18809.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.036272 restraints weight = 15243.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11756  Z= 0.155
  Angle     :  0.559  11.374  16509  Z= 0.302
  Chirality :  0.036   0.134   1904
  Planarity :  0.004   0.061   1565
  Dihedral  : 19.124 171.783   3095
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  8.07 %
    Favored  : 90.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.27), residues: 985
  helix:  1.93 (0.24), residues: 487
  sheet:  1.78 (0.60), residues: 80
  loop :  0.20 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  71 
 TYR   0.016   0.002   TYR A 656 
 PHE   0.011   0.001   PHE A 970 
 TRP   0.004   0.001   TRP A 464 
 HIS   0.008   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (11756)
  covalent geometry    : angle       0.55896 (16509)
  hydrogen bonds       : bond        0.05123 (  503)
  hydrogen bonds       : angle       4.35291 ( 1331)

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 ARG cc_start: 0.9593 (mtm180) cc_final: 0.9085 (mtp85)
REVERT: A   90 MET cc_start: 0.9205 (tpp) cc_final: 0.8736 (tpt)
REVERT: A  335 LEU cc_start: 0.9898 (OUTLIER) cc_final: 0.9643 (pp)
REVERT: A  448 ILE cc_start: 0.9660 (mt) cc_final: 0.9408 (tp)
REVERT: A  471 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7822 (pm20)
REVERT: A  473 ILE cc_start: 0.9740 (mt) cc_final: 0.9235 (tp)
REVERT: A  534 MET cc_start: 0.6676 (mtt) cc_final: 0.5384 (ttm)
REVERT: A  562 LYS cc_start: 0.9401 (tttt) cc_final: 0.9088 (tppt)
REVERT: A  671 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.8889 (tmt170)
REVERT: A  722 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8779 (mp0)
REVERT: A  746 GLU cc_start: 0.9396 (tt0) cc_final: 0.9097 (tt0)
REVERT: A 1089 MET cc_start: 0.9121 (tpp) cc_final: 0.8726 (mmm)
REVERT: A 1228 LEU cc_start: 0.9107 (tp) cc_final: 0.8518 (tt)
  outliers start: 15
  outliers final: 9
  residues processed: 129
  average time/residue: 0.1261
  time to fit residues: 22.5471
Evaluate side-chains
  103 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  671 ARG
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1095 VAL
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1153 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 50 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 95 optimal weight:    8.9990
   chunk 108 optimal weight:   10.0000
   chunk 99 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 98 optimal weight:    9.9990
   chunk 34 optimal weight:    0.6980
   chunk 84 optimal weight:   10.0000
   chunk 82 optimal weight:    6.9990
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 612 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.042201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.031043 restraints weight = 86233.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.032304 restraints weight = 42717.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.033180 restraints weight = 27510.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2669 r_free = 0.2669 target = 0.033738 restraints weight = 20413.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.034134 restraints weight = 16758.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.3356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11756  Z= 0.195
  Angle     :  0.556   8.324  16509  Z= 0.304
  Chirality :  0.037   0.154   1904
  Planarity :  0.004   0.059   1565
  Dihedral  : 19.297 173.649   3095
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  8.41 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.27), residues: 985
  helix:  1.65 (0.24), residues: 486
  sheet:  1.77 (0.59), residues: 80
  loop :  0.20 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  71 
 TYR   0.012   0.002   TYR A1356 
 PHE   0.014   0.002   PHE A 970 
 TRP   0.012   0.001   TRP A 464 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (11756)
  covalent geometry    : angle       0.55575 (16509)
  hydrogen bonds       : bond        0.04988 (  503)
  hydrogen bonds       : angle       4.35132 ( 1331)

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.9483 (ttp-170) cc_final: 0.8893 (ptp-110)
REVERT: A   71 ARG cc_start: 0.9573 (mtm180) cc_final: 0.9125 (mtp85)
REVERT: A   90 MET cc_start: 0.9370 (tpp) cc_final: 0.9054 (tpp)
REVERT: A  161 MET cc_start: 0.9513 (mpp) cc_final: 0.9306 (mmm)
REVERT: A  335 LEU cc_start: 0.9905 (tt) cc_final: 0.9676 (pp)
REVERT: A  399 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9427 (tp)
REVERT: A  448 ILE cc_start: 0.9621 (mt) cc_final: 0.9369 (tp)
REVERT: A  534 MET cc_start: 0.7045 (mtt) cc_final: 0.5814 (ttm)
REVERT: A  558 LYS cc_start: 0.9569 (mttt) cc_final: 0.9224 (ttpp)
REVERT: A  722 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8890 (mp0)
REVERT: A  746 GLU cc_start: 0.9418 (tt0) cc_final: 0.9121 (tt0)
REVERT: A  763 MET cc_start: 0.4973 (tmm) cc_final: 0.3822 (mtt)
REVERT: A  939 MET cc_start: 0.9698 (mmm) cc_final: 0.9371 (mmm)
REVERT: A 1089 MET cc_start: 0.9132 (tpp) cc_final: 0.8652 (tpp)
REVERT: A 1097 LYS cc_start: 0.9371 (tttm) cc_final: 0.8921 (tptt)
REVERT: A 1099 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7760 (mp0)
REVERT: A 1228 LEU cc_start: 0.9191 (tp) cc_final: 0.8854 (tt)
  outliers start: 18
  outliers final: 12
  residues processed: 105
  average time/residue: 0.1188
  time to fit residues: 17.6493
Evaluate side-chains
  101 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  461 ARG
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1095 VAL
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1153 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 45 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 106 optimal weight:   20.0000
   chunk 52 optimal weight:    3.9990
   chunk 5 optimal weight:   20.0000
   chunk 51 optimal weight:    4.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1264 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 = 0.2943 r_free = 0.2943 target = 0.041329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2569 r_free = 0.2569 target = 0.030335 restraints weight = 86655.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.031589 restraints weight = 42492.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.032439 restraints weight = 27271.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.032988 restraints weight = 20236.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.033387 restraints weight = 16635.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  11756  Z= 0.186
  Angle     :  0.536   6.663  16509  Z= 0.296
  Chirality :  0.036   0.138   1904
  Planarity :  0.004   0.055   1565
  Dihedral  : 19.407 176.170   3095
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 10.43 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.27), residues: 985
  helix:  1.59 (0.24), residues: 486
  sheet:  1.88 (0.59), residues: 80
  loop :  0.25 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 395 
 TYR   0.014   0.001   TYR A1356 
 PHE   0.014   0.001   PHE A 970 
 TRP   0.009   0.001   TRP A 464 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (11756)
  covalent geometry    : angle       0.53579 (16509)
  hydrogen bonds       : bond        0.04863 (  503)
  hydrogen bonds       : angle       4.25888 ( 1331)

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.9465 (ttp-170) cc_final: 0.9167 (ptm160)
REVERT: A   71 ARG cc_start: 0.9533 (mtm180) cc_final: 0.9304 (mtp85)
REVERT: A   90 MET cc_start: 0.9418 (tpp) cc_final: 0.9072 (tpp)
REVERT: A  161 MET cc_start: 0.9514 (mpp) cc_final: 0.9289 (mpp)
REVERT: A  335 LEU cc_start: 0.9904 (OUTLIER) cc_final: 0.9667 (pp)
REVERT: A  448 ILE cc_start: 0.9589 (mt) cc_final: 0.9364 (tp)
REVERT: A  498 PHE cc_start: 0.9112 (m-80) cc_final: 0.8805 (m-80)
REVERT: A  534 MET cc_start: 0.7598 (mtt) cc_final: 0.6437 (ttm)
REVERT: A  585 ASP cc_start: 0.9026 (t0) cc_final: 0.8739 (p0)
REVERT: A  722 GLU cc_start: 0.9320 (mt-10) cc_final: 0.8954 (mp0)
REVERT: A  739 GLN cc_start: 0.9780 (mm-40) cc_final: 0.9326 (mm-40)
REVERT: A  746 GLU cc_start: 0.9476 (tt0) cc_final: 0.9103 (tt0)
REVERT: A  747 LEU cc_start: 0.9670 (mm) cc_final: 0.9431 (mt)
REVERT: A  763 MET cc_start: 0.5479 (tmm) cc_final: 0.4164 (mtt)
REVERT: A  939 MET cc_start: 0.9756 (mmm) cc_final: 0.9476 (mmm)
REVERT: A 1089 MET cc_start: 0.9172 (tpp) cc_final: 0.8724 (tpp)
REVERT: A 1097 LYS cc_start: 0.9326 (tttm) cc_final: 0.8895 (tttt)
REVERT: A 1099 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7962 (mm-30)
REVERT: A 1228 LEU cc_start: 0.9196 (tp) cc_final: 0.8846 (tt)
  outliers start: 19
  outliers final: 12
  residues processed: 103
  average time/residue: 0.1219
  time to fit residues: 17.5923
Evaluate side-chains
  91 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  461 ARG
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1095 VAL
Chi-restraints excluded: chain A residue 1153 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 102 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 82 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 110 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 369 GLN
** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.039163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2515 r_free = 0.2515 target = 0.028500 restraints weight = 89254.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2553 r_free = 0.2553 target = 0.029656 restraints weight = 44153.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.030455 restraints weight = 28847.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.030968 restraints weight = 21557.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.031350 restraints weight = 17853.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          0.4859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  11756  Z= 0.273
  Angle     :  0.617   6.403  16509  Z= 0.340
  Chirality :  0.038   0.137   1904
  Planarity :  0.004   0.057   1565
  Dihedral  : 19.730 177.836   3095
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 11.21 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.26), residues: 985
  helix:  1.01 (0.23), residues: 484
  sheet:  1.89 (0.60), residues: 70
  loop :  0.04 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  71 
 TYR   0.020   0.002   TYR A1356 
 PHE   0.034   0.002   PHE A 693 
 TRP   0.012   0.002   TRP A 464 
 HIS   0.008   0.002   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 (11756)
  covalent geometry    : angle       0.61714 (16509)
  hydrogen bonds       : bond        0.05687 (  503)
  hydrogen bonds       : angle       4.57624 ( 1331)

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8312 (mm-30)
REVERT: A   71 ARG cc_start: 0.9459 (mtm180) cc_final: 0.9005 (mtp85)
REVERT: A   90 MET cc_start: 0.9384 (tpp) cc_final: 0.9024 (tpp)
REVERT: A  125 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8192 (mm-30)
REVERT: A  335 LEU cc_start: 0.9905 (OUTLIER) cc_final: 0.9693 (pp)
REVERT: A  380 LEU cc_start: 0.9765 (OUTLIER) cc_final: 0.9558 (tp)
REVERT: A  495 MET cc_start: 0.9443 (mmm) cc_final: 0.9010 (ttm)
REVERT: A  534 MET cc_start: 0.8009 (mtt) cc_final: 0.7226 (ttm)
REVERT: A  722 GLU cc_start: 0.9472 (mt-10) cc_final: 0.9105 (mp0)
REVERT: A  739 GLN cc_start: 0.9809 (mm-40) cc_final: 0.9438 (mm-40)
REVERT: A  746 GLU cc_start: 0.9526 (tt0) cc_final: 0.9151 (tt0)
REVERT: A  939 MET cc_start: 0.9771 (mmm) cc_final: 0.9515 (mmm)
REVERT: A 1089 MET cc_start: 0.9193 (tpp) cc_final: 0.8781 (tpp)
  outliers start: 24
  outliers final: 17
  residues processed: 94
  average time/residue: 0.1084
  time to fit residues: 14.4930
Evaluate side-chains
  89 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  461 ARG
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue  975 VAL
Chi-restraints excluded: chain A residue 1153 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 87 optimal weight:    8.9990
   chunk 67 optimal weight:   10.0000
   chunk 95 optimal weight:   10.0000
   chunk 45 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 80 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A1264 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 = 0.2881 r_free = 0.2881 target = 0.039209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2513 r_free = 0.2513 target = 0.028575 restraints weight = 87487.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2551 r_free = 0.2551 target = 0.029762 restraints weight = 42395.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2578 r_free = 0.2578 target = 0.030580 restraints weight = 27210.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.031137 restraints weight = 20205.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.031549 restraints weight = 16544.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.5128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  11756  Z= 0.235
  Angle     :  0.592   7.763  16509  Z= 0.325
  Chirality :  0.038   0.169   1904
  Planarity :  0.004   0.054   1565
  Dihedral  : 19.761 179.180   3095
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 13.12 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.26), residues: 985
  helix:  0.99 (0.23), residues: 485
  sheet:  2.01 (0.59), residues: 70
  loop :  0.07 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  71 
 TYR   0.014   0.002   TYR A 594 
 PHE   0.025   0.002   PHE A 693 
 TRP   0.008   0.001   TRP A 464 
 HIS   0.008   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (11756)
  covalent geometry    : angle       0.59159 (16509)
  hydrogen bonds       : bond        0.05224 (  503)
  hydrogen bonds       : angle       4.57730 ( 1331)

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8286 (mm-30)
REVERT: A   71 ARG cc_start: 0.9464 (mtm180) cc_final: 0.8977 (mtp85)
REVERT: A   90 MET cc_start: 0.9415 (tpp) cc_final: 0.9034 (tpp)
REVERT: A  125 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8178 (mm-30)
REVERT: A  161 MET cc_start: 0.9526 (mpp) cc_final: 0.9312 (mmt)
REVERT: A  321 MET cc_start: 0.9319 (mmm) cc_final: 0.8838 (mmm)
REVERT: A  335 LEU cc_start: 0.9904 (OUTLIER) cc_final: 0.9697 (pp)
REVERT: A  495 MET cc_start: 0.9435 (mmm) cc_final: 0.9111 (ttp)
REVERT: A  534 MET cc_start: 0.8339 (mtt) cc_final: 0.7458 (ttm)
REVERT: A  558 LYS cc_start: 0.9356 (mttt) cc_final: 0.8975 (mtpt)
REVERT: A  722 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9129 (mp0)
REVERT: A  739 GLN cc_start: 0.9762 (mm-40) cc_final: 0.9407 (mm-40)
REVERT: A  746 GLU cc_start: 0.9509 (tt0) cc_final: 0.9218 (tt0)
REVERT: A  939 MET cc_start: 0.9755 (mmm) cc_final: 0.9508 (mmm)
REVERT: A 1089 MET cc_start: 0.9219 (tpp) cc_final: 0.8819 (tpp)
REVERT: A 1169 MET cc_start: 0.9284 (mmm) cc_final: 0.9066 (tpt)
REVERT: A 1213 MET cc_start: 0.9355 (tpp) cc_final: 0.9131 (tpp)
  outliers start: 19
  outliers final: 14
  residues processed: 88
  average time/residue: 0.0981
  time to fit residues: 12.7444
Evaluate side-chains
  86 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  461 ARG
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1095 VAL
Chi-restraints excluded: chain A residue 1153 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 26 optimal weight:    8.9990
   chunk 11 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9990
   chunk 46 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 985 HIS
A1101 GLN
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1264 HIS ** 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 = 0.2862 r_free = 0.2862 target = 0.038481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2497 r_free = 0.2497 target = 0.028046 restraints weight = 90014.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2534 r_free = 0.2534 target = 0.029214 restraints weight = 43309.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2562 r_free = 0.2562 target = 0.030001 restraints weight = 27742.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.030543 restraints weight = 20586.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.030879 restraints weight = 16867.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.2578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.5604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  11756  Z= 0.271
  Angle     :  0.630   8.382  16509  Z= 0.344
  Chirality :  0.039   0.172   1904
  Planarity :  0.004   0.055   1565
  Dihedral  : 19.939 178.771   3095
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 17.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.12 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.26), residues: 985
  helix:  0.61 (0.23), residues: 491
  sheet:  1.78 (0.59), residues: 72
  loop : -0.09 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 403 
 TYR   0.015   0.002   TYR A1356 
 PHE   0.021   0.002   PHE A 693 
 TRP   0.008   0.002   TRP A 464 
 HIS   0.007   0.002   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (11756)
  covalent geometry    : angle       0.62996 (16509)
  hydrogen bonds       : bond        0.05610 (  503)
  hydrogen bonds       : angle       4.73806 ( 1331)

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8306 (mm-30)
REVERT: A   90 MET cc_start: 0.9446 (tpp) cc_final: 0.9016 (tpp)
REVERT: A  125 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8160 (mm-30)
REVERT: A  161 MET cc_start: 0.9510 (mpp) cc_final: 0.9263 (mmt)
REVERT: A  335 LEU cc_start: 0.9905 (OUTLIER) cc_final: 0.9689 (pp)
REVERT: A  495 MET cc_start: 0.9384 (mmm) cc_final: 0.9088 (ttm)
REVERT: A  534 MET cc_start: 0.8468 (mtt) cc_final: 0.7586 (ttm)
REVERT: A  558 LYS cc_start: 0.9363 (mttt) cc_final: 0.8932 (mmmm)
REVERT: A  631 MET cc_start: 0.9184 (mmm) cc_final: 0.8463 (mmm)
REVERT: A  722 GLU cc_start: 0.9550 (mt-10) cc_final: 0.9217 (mp0)
REVERT: A  739 GLN cc_start: 0.9770 (mm-40) cc_final: 0.9428 (mm-40)
REVERT: A  746 GLU cc_start: 0.9556 (tt0) cc_final: 0.9211 (tt0)
REVERT: A  747 LEU cc_start: 0.9746 (mm) cc_final: 0.9478 (mt)
REVERT: A  929 LYS cc_start: 0.9227 (mttt) cc_final: 0.9020 (mttm)
REVERT: A  939 MET cc_start: 0.9767 (mmm) cc_final: 0.9538 (mmm)
REVERT: A 1089 MET cc_start: 0.9237 (tpp) cc_final: 0.8846 (tpp)
REVERT: A 1213 MET cc_start: 0.9426 (tpp) cc_final: 0.9185 (tpp)
  outliers start: 24
  outliers final: 18
  residues processed: 89
  average time/residue: 0.1247
  time to fit residues: 15.5592
Evaluate side-chains
  88 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  461 ARG
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  562 LYS
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1153 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 102 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 111 optimal weight:   10.0000
   chunk 64 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   chunk 95 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 89 optimal weight:    8.9990
   chunk 93 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A1264 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 = 0.2883 r_free = 0.2883 target = 0.039218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2517 r_free = 0.2517 target = 0.028635 restraints weight = 87473.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.029843 restraints weight = 41967.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.030619 restraints weight = 26751.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.031198 restraints weight = 19944.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.031543 restraints weight = 16263.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.5678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11756  Z= 0.194
  Angle     :  0.569   7.043  16509  Z= 0.313
  Chirality :  0.037   0.195   1904
  Planarity :  0.004   0.053   1565
  Dihedral  : 19.910 176.848   3095
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.01 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.27), residues: 985
  helix:  1.04 (0.23), residues: 479
  sheet:  1.79 (0.59), residues: 72
  loop :  0.20 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 403 
 TYR   0.011   0.001   TYR A 639 
 PHE   0.019   0.001   PHE A 693 
 TRP   0.009   0.001   TRP A 464 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (11756)
  covalent geometry    : angle       0.56909 (16509)
  hydrogen bonds       : bond        0.05008 (  503)
  hydrogen bonds       : angle       4.47850 ( 1331)

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8275 (mm-30)
REVERT: A   90 MET cc_start: 0.9436 (tpp) cc_final: 0.8919 (tpp)
REVERT: A  125 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8217 (mm-30)
REVERT: A  161 MET cc_start: 0.9507 (mpp) cc_final: 0.9232 (mmt)
REVERT: A  335 LEU cc_start: 0.9899 (OUTLIER) cc_final: 0.9675 (pp)
REVERT: A  383 MET cc_start: 0.8187 (mmp) cc_final: 0.7934 (mmp)
REVERT: A  495 MET cc_start: 0.9380 (mmm) cc_final: 0.9139 (ttp)
REVERT: A  534 MET cc_start: 0.8303 (mtt) cc_final: 0.7483 (ttm)
REVERT: A  558 LYS cc_start: 0.9373 (mttt) cc_final: 0.8978 (mmmm)
REVERT: A  631 MET cc_start: 0.9217 (mmm) cc_final: 0.8566 (mmm)
REVERT: A  722 GLU cc_start: 0.9552 (mt-10) cc_final: 0.9241 (mp0)
REVERT: A  746 GLU cc_start: 0.9528 (tt0) cc_final: 0.9237 (tt0)
REVERT: A  747 LEU cc_start: 0.9774 (mm) cc_final: 0.9521 (mt)
REVERT: A  939 MET cc_start: 0.9763 (mmm) cc_final: 0.9532 (mmm)
REVERT: A  977 GLU cc_start: 0.9122 (pm20) cc_final: 0.8790 (pm20)
REVERT: A 1089 MET cc_start: 0.9243 (tpp) cc_final: 0.8845 (tpp)
REVERT: A 1213 MET cc_start: 0.9381 (tpp) cc_final: 0.9121 (tpp)
  outliers start: 20
  outliers final: 15
  residues processed: 88
  average time/residue: 0.1136
  time to fit residues: 14.4948
Evaluate side-chains
  87 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LYS
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  461 ARG
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain A residue  648 MET
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1153 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.1980
   chunk 48 optimal weight:    8.9990
   chunk 45 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 73 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 47 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   overall best weight:    5.8388

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.038685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2505 r_free = 0.2505 target = 0.028209 restraints weight = 88873.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2543 r_free = 0.2543 target = 0.029387 restraints weight = 43003.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2570 r_free = 0.2570 target = 0.030160 restraints weight = 27663.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.030685 restraints weight = 20617.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.031068 restraints weight = 16979.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.2588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.5884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  11756  Z= 0.230
  Angle     :  0.605  12.295  16509  Z= 0.331
  Chirality :  0.038   0.226   1904
  Planarity :  0.004   0.053   1565
  Dihedral  : 19.979 178.760   3095
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.90 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.27), residues: 985
  helix:  0.88 (0.23), residues: 477
  sheet:  1.68 (0.58), residues: 72
  loop :  0.13 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 340 
 TYR   0.012   0.002   TYR A1356 
 PHE   0.018   0.002   PHE A 693 
 TRP   0.008   0.001   TRP A 464 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (11756)
  covalent geometry    : angle       0.60493 (16509)
  hydrogen bonds       : bond        0.05346 (  503)
  hydrogen bonds       : angle       4.59070 ( 1331)

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8302 (mm-30)
REVERT: A   90 MET cc_start: 0.9445 (tpp) cc_final: 0.8905 (tpp)
REVERT: A  125 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8174 (mm-30)
REVERT: A  161 MET cc_start: 0.9530 (mpp) cc_final: 0.9218 (mmt)
REVERT: A  335 LEU cc_start: 0.9904 (OUTLIER) cc_final: 0.9686 (pp)
REVERT: A  495 MET cc_start: 0.9369 (mmm) cc_final: 0.9120 (ttm)
REVERT: A  534 MET cc_start: 0.8357 (mtt) cc_final: 0.7614 (ttm)
REVERT: A  558 LYS cc_start: 0.9386 (mttt) cc_final: 0.9163 (mtpp)
REVERT: A  586 ARG cc_start: 0.8925 (ttm-80) cc_final: 0.8705 (tpt-90)
REVERT: A  631 MET cc_start: 0.9240 (mmm) cc_final: 0.8631 (mmm)
REVERT: A  722 GLU cc_start: 0.9603 (mt-10) cc_final: 0.9277 (mp0)
REVERT: A  746 GLU cc_start: 0.9543 (tt0) cc_final: 0.9263 (tt0)
REVERT: A  939 MET cc_start: 0.9768 (mmm) cc_final: 0.9546 (mmm)
REVERT: A 1089 MET cc_start: 0.9229 (tpp) cc_final: 0.8844 (tpp)
REVERT: A 1213 MET cc_start: 0.9428 (tpp) cc_final: 0.9164 (tpp)
  outliers start: 22
  outliers final: 17
  residues processed: 84
  average time/residue: 0.1121
  time to fit residues: 13.5398
Evaluate side-chains
  86 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LYS
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  461 ARG
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  562 LYS
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1153 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 72 optimal weight:    1.9990
   chunk 101 optimal weight:   10.0000
   chunk 102 optimal weight:   10.0000
   chunk 99 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 90 optimal weight:    5.9990
   chunk 56 optimal weight:   20.0000
   chunk 30 optimal weight:    0.9980
   chunk 45 optimal weight:    8.9990
   chunk 54 optimal weight:   20.0000
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A1264 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 = 0.2881 r_free = 0.2881 target = 0.038663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2519 r_free = 0.2519 target = 0.028230 restraints weight = 89953.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2556 r_free = 0.2556 target = 0.029389 restraints weight = 43646.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.030207 restraints weight = 27960.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.030712 restraints weight = 20790.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.031086 restraints weight = 17164.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.2600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8749
moved from start:          0.5974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11756  Z= 0.221
  Angle     :  0.616  11.672  16509  Z= 0.335
  Chirality :  0.038   0.239   1904
  Planarity :  0.004   0.053   1565
  Dihedral  : 20.010 178.268   3095
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 15.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.57 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.27), residues: 985
  helix:  0.85 (0.23), residues: 485
  sheet:  1.66 (0.58), residues: 72
  loop :  0.04 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 403 
 TYR   0.011   0.002   TYR A1356 
 PHE   0.019   0.001   PHE A 693 
 TRP   0.009   0.001   TRP A 464 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (11756)
  covalent geometry    : angle       0.61561 (16509)
  hydrogen bonds       : bond        0.05255 (  503)
  hydrogen bonds       : angle       4.59129 ( 1331)

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

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

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1970 Ramachandran restraints generated.
    985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8312 (mm-30)
REVERT: A   90 MET cc_start: 0.9404 (tpp) cc_final: 0.8856 (tpp)
REVERT: A  125 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8241 (mm-30)
REVERT: A  161 MET cc_start: 0.9482 (mpp) cc_final: 0.9205 (mmt)
REVERT: A  335 LEU cc_start: 0.9899 (OUTLIER) cc_final: 0.9677 (pp)
REVERT: A  383 MET cc_start: 0.8388 (mmp) cc_final: 0.8181 (mmp)
REVERT: A  534 MET cc_start: 0.8196 (mtt) cc_final: 0.7499 (ttm)
REVERT: A  558 LYS cc_start: 0.9393 (mttt) cc_final: 0.9162 (mtpp)
REVERT: A  586 ARG cc_start: 0.8903 (ttm-80) cc_final: 0.8678 (tpt-90)
REVERT: A  631 MET cc_start: 0.9202 (mmm) cc_final: 0.8573 (mmm)
REVERT: A  722 GLU cc_start: 0.9616 (mt-10) cc_final: 0.9301 (mp0)
REVERT: A  739 GLN cc_start: 0.9794 (mm-40) cc_final: 0.9405 (mm-40)
REVERT: A  746 GLU cc_start: 0.9523 (tt0) cc_final: 0.9214 (tt0)
REVERT: A  939 MET cc_start: 0.9796 (mmm) cc_final: 0.9567 (mmm)
REVERT: A 1089 MET cc_start: 0.9256 (tpp) cc_final: 0.8871 (tpp)
REVERT: A 1213 MET cc_start: 0.9429 (tpp) cc_final: 0.9156 (tpp)
REVERT: A 1226 LEU cc_start: 0.9663 (tt) cc_final: 0.9439 (tt)
  outliers start: 19
  outliers final: 16
  residues processed: 84
  average time/residue: 0.1220
  time to fit residues: 14.6519
Evaluate side-chains
  85 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LYS
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  461 ARG
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  562 LYS
Chi-restraints excluded: chain A residue  646 LYS
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1153 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 3 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 40 optimal weight:    7.9990
   chunk 105 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 75 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   overall best weight:    7.1992

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

Flipped N/Q/H residues before XYZ refinement:
** A1264 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 = 0.2855 r_free = 0.2855 target = 0.037985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2487 r_free = 0.2487 target = 0.027585 restraints weight = 91716.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2525 r_free = 0.2525 target = 0.028739 restraints weight = 43932.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2550 r_free = 0.2550 target = 0.029495 restraints weight = 28102.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2569 r_free = 0.2569 target = 0.030039 restraints weight = 21007.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.030405 restraints weight = 17225.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.6122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  11756  Z= 0.277
  Angle     :  0.665  10.618  16509  Z= 0.360
  Chirality :  0.040   0.261   1904
  Planarity :  0.004   0.053   1565
  Dihedral  : 20.108 179.402   3095
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 18.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.46 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.26), residues: 985
  helix:  0.66 (0.23), residues: 484
  sheet:  1.51 (0.58), residues: 72
  loop : -0.05 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 403 
 TYR   0.015   0.002   TYR A1356 
 PHE   0.017   0.002   PHE A 693 
 TRP   0.008   0.002   TRP A 476 
 HIS   0.006   0.002   HIS A1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 (11756)
  covalent geometry    : angle       0.66462 (16509)
  hydrogen bonds       : bond        0.05694 (  503)
  hydrogen bonds       : angle       4.77341 ( 1331)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1622.03 seconds
wall clock time: 29 minutes 6.57 seconds (1746.57 seconds total)