Starting phenix.real_space_refine
on Fri Jul  3 02:55:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k4c_62054/07_2026/9k4c_62054.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k4c_62054/07_2026/9k4c_62054.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k4c_62054/07_2026/9k4c_62054.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k4c_62054/07_2026/9k4c_62054.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k4c_62054/07_2026/9k4c_62054.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k4c_62054/07_2026/9k4c_62054.map"
  }
  resolution = 3.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     149      5.49       5
     S      18      5.16       5
     C    6781      2.51       5
     N    2039      2.21       5
     O    2538      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11525
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1015, 8326
          Classifications: {'peptide': 1015}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 988}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 783
          Classifications: {'DNA': 38}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 37}
    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: 2111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 2111
          Classifications: {'RNA': 99}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 49, 'rna3p_pyr': 39}
          Link IDs: {'rna2p': 11, 'rna3p': 87}
  Time building chain proxies: 2.59, per 1000 atoms: 0.22
  Number of scatterers: 11525
  At special positions: 0
  Unit cell: (120.288, 115.992, 111.696, 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      18     16.00
     P     149     15.00
     O    2538      8.00
     N    2039      7.00
     C    6781      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 428.4 milliseconds
  

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1932

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 6 sheets defined
      56.1% alpha, 8.2% beta
      54 base pairs and 80 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 4.754A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.356A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.561A  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 121 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.639A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.521A  pdb=" N   PHE A 164 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 306
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.638A  pdb=" N   ALA A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 352
      removed outlier: 4.408A  pdb=" N   LYS A 348 " --> pdb=" O   PRO A 344 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   GLU A 349 " --> pdb=" O   GLU A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 383
      Proline residue:  A 378  - end of helix
      removed outlier: 3.658A  pdb=" N   MET A 383 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 396
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.665A  pdb=" N   ASN A 407 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.288A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 477 through 482
      removed outlier: 3.670A  pdb=" N   VAL A 481 " --> pdb=" O   ASN A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 4.046A  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 602
    Processing helix  chain 'A' and resid 603 through 609
    Processing helix  chain 'A' and resid 612 through 626
      removed outlier: 3.522A  pdb=" N   PHE A 626 " --> pdb=" O   THR A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 643
      removed outlier: 4.745A  pdb=" N   HIS A 641 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 654
      removed outlier: 3.664A  pdb=" N   ARG A 654 " --> pdb=" O   GLN A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 669
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 686 through 690
      removed outlier: 4.244A  pdb=" N   ALA A 689 " --> pdb=" O   ASP A 686 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ASN A 690 " --> pdb=" O   GLY A 687 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 686 through 690'
    Processing helix  chain 'A' and resid 692 through 699
      removed outlier: 3.559A  pdb=" N   ILE A 697 " --> pdb=" O   PHE A 693 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   HIS A 698 " --> pdb=" O   MET A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 712
      removed outlier: 4.426A  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: 3.699A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   MET A 751 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 917 through 940
      removed outlier: 3.923A  pdb=" N   LEU A 921 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   THR A 928 " --> pdb=" O   THR A 924 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   LYS A 929 " --> pdb=" O   ARG A 925 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   HIS A 930 " --> pdb=" O   GLN A 926 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASN A 940 " --> pdb=" O   ASP A 936 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 970
      removed outlier: 4.260A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 999
      removed outlier: 3.634A  pdb=" N   LEU A 997 " --> pdb=" O   VAL A 993 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ILE A 998 " --> pdb=" O   GLY A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
      removed outlier: 3.760A  pdb=" N   ASN A1177 " --> pdb=" O   SER A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1185
    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: 3.526A  pdb=" N   HIS A1262 " --> pdb=" O   PHE A1258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.614A  pdb=" N   GLU A1268 " --> pdb=" O   HIS A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1313
      removed outlier: 3.606A  pdb=" N   HIS A1311 " --> pdb=" O   GLU A1307 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU A1312 " --> pdb=" O   ASN A1308 " (cutoff:3.500A)
      removed outlier: 3.919A  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 1339 through 1344
      removed outlier: 3.644A  pdb=" N   VAL A1342 " --> pdb=" O   THR A1339 " (cutoff:3.500A)
      removed outlier: 4.063A  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: 3.508A  pdb=" N   TRP A  18 " --> pdb=" O   GLY A  49 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL A1095 " --> pdb=" O   ALA A  50 " (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: 6.738A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 8.371A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 531
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 5.045A  pdb=" N   LYS A1156 " --> pdb=" O   GLU A1150 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   GLU A1150 " --> pdb=" O   LYS A1156 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   LYS A1158 " --> pdb=" O   LYS A1148 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   LYS A1148 " --> pdb=" O   LYS A1158 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   VAL A1160 " --> pdb=" O   VAL A1146 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   VAL A1146 " --> pdb=" O   VAL A1160 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   GLU A1162 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
      removed outlier: 5.113A  pdb=" N   LEU A1144 " --> pdb=" O   GLU A1162 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LEU A1164 " --> pdb=" O   SER A1142 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   SER A1142 " --> pdb=" O   LEU A1164 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ILE A1166 " --> pdb=" O   ALA A1140 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1324 through 1326
      removed outlier: 3.890A  pdb=" N   PHE A1324 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)

    379 hydrogen bonds defined for protein.
    1104 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      136 hydrogen bonds
      264 hydrogen bond angles
      0 basepair planarities
      54 basepair parallelities
      80 stacking parallelities
  Total time for adding SS restraints: 2.71

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1942
        1.33 -     1.45: 3733
        1.45 -     1.57: 6055
        1.57 -     1.69: 298
        1.69 -     1.81: 34
  Bond restraints: 12062
  Sorted by residual:
  bond pdb=" C3'  DG B  38 "
       pdb=" C2'  DG B  38 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.36e+00
  bond pdb=" C3'  DC B  16 "
       pdb=" C2'  DC B  16 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.32e+00
  bond pdb=" C3'  DC B  14 "
       pdb=" C2'  DC B  14 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.91e+00
  bond pdb=" C3'  DC C   5 "
       pdb=" C2'  DC C   5 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.79e+00
  bond pdb=" C3'  DT B   4 "
       pdb=" C2'  DT B   4 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.34e+00
  ... (remaining 12057 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 16139
        1.21 -     2.43: 713
        2.43 -     3.64: 86
        3.64 -     4.85: 7
        4.85 -     6.07: 3
  Bond angle restraints: 16948
  Sorted by residual:
  angle pdb=" O4'  DG B  18 "
        pdb=" C4'  DG B  18 "
        pdb=" C3'  DG B  18 "
      ideal   model   delta    sigma   weight residual
     106.00  102.94    3.06 6.00e-01 2.78e+00 2.60e+01
  angle pdb=" O4'  DG B  23 "
        pdb=" C4'  DG B  23 "
        pdb=" C3'  DG B  23 "
      ideal   model   delta    sigma   weight residual
     106.00  103.22    2.78 6.00e-01 2.78e+00 2.15e+01
  angle pdb=" O4'  DA B  22 "
        pdb=" C4'  DA B  22 "
        pdb=" C3'  DA B  22 "
      ideal   model   delta    sigma   weight residual
     106.00  103.32    2.68 6.00e-01 2.78e+00 2.00e+01
  angle pdb=" N3   DT B  36 "
        pdb=" C4   DT B  36 "
        pdb=" O4   DT B  36 "
      ideal   model   delta    sigma   weight residual
     119.90  122.54   -2.64 6.00e-01 2.78e+00 1.94e+01
  angle pdb=" O4'  DT B  19 "
        pdb=" C4'  DT B  19 "
        pdb=" C3'  DT B  19 "
      ideal   model   delta    sigma   weight residual
     106.00  103.42    2.58 6.00e-01 2.78e+00 1.85e+01
  ... (remaining 16943 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.19: 6798
       29.19 -    58.38: 383
       58.38 -    87.57: 91
       87.57 -   116.75: 0
      116.75 -   145.94: 1
  Dihedral angle restraints: 7273
    sinusoidal: 4290
      harmonic: 2983
  Sorted by residual:
  dihedral pdb=" CA  ILE A 927 "
           pdb=" C   ILE A 927 "
           pdb=" N   THR A 928 "
           pdb=" CA  THR A 928 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.78  -24.22     0      5.00e+00 4.00e-02 2.35e+01
  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   74.06  145.94     1      3.50e+01 8.16e-04 1.43e+01
  dihedral pdb=" CA  PHE A  86 "
           pdb=" C   PHE A  86 "
           pdb=" N   SER A  87 "
           pdb=" CA  SER A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.60  -16.40     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 7270 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1353
       0.031 -    0.061: 400
       0.061 -    0.092: 135
       0.092 -    0.122: 66
       0.122 -    0.153: 5
  Chirality restraints: 1959
  Sorted by residual:
  chirality pdb=" C1'   A D  67 "
            pdb=" O4'   A D  67 "
            pdb=" C2'   A D  67 "
            pdb=" N9    A D  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.30    0.15 2.00e-01 2.50e+01 5.84e-01
  chirality pdb=" CA  VAL A  27 "
            pdb=" N   VAL A  27 "
            pdb=" C   VAL A  27 "
            pdb=" CB  VAL A  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" C3'  DG B   7 "
            pdb=" C4'  DG B   7 "
            pdb=" O3'  DG B   7 "
            pdb=" C2'  DG B   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.60   -0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 1956 not shown)

  Planarity restraints: 1601
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1228 "   -0.027 5.00e-02 4.00e+02   4.15e-02 2.76e+00
        pdb=" N   PRO A1229 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A1229 "   -0.021 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  67 "    0.022 2.00e-02 2.50e+03   9.81e-03 2.65e+00
        pdb=" N9    A D  67 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8    A D  67 "   -0.007 2.00e-02 2.50e+03
        pdb=" N7    A D  67 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    A D  67 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A D  67 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A D  67 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    A D  67 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2    A D  67 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    A D  67 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  67 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U D  68 "    0.016 2.00e-02 2.50e+03   8.74e-03 1.72e+00
        pdb=" N1    U D  68 "   -0.020 2.00e-02 2.50e+03
        pdb=" C2    U D  68 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2    U D  68 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    U D  68 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    U D  68 "    0.002 2.00e-02 2.50e+03
        pdb=" O4    U D  68 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    U D  68 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    U D  68 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1598 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 3
        2.02 -     2.74: 917
        2.74 -     3.46: 15378
        3.46 -     4.18: 28686
        4.18 -     4.90: 45719
  Nonbonded interactions: 90703
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A  44 "
            pdb=" O6    G D  94 "
     model   vdw
     1.298 3.120
  nonbonded pdb=" NH1 ARG A 340 "
            pdb=" OP1   A D  43 "
     model   vdw
     1.298 3.120
  nonbonded pdb=" NH1 ARG A  71 "
            pdb=" N4    C D  20 "
     model   vdw
     1.352 3.200
  nonbonded pdb=" O2   DC B  16 "
            pdb=" N2    G D  22 "
     model   vdw
     2.095 2.496
  nonbonded pdb=" NH1 ARG A  71 "
            pdb=" C4    C D  20 "
     model   vdw
     2.172 3.340
  ... (remaining 90698 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:             0.490
  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:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.940
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12062  Z= 0.267
  Angle     :  0.550   6.069  16948  Z= 0.449
  Chirality :  0.037   0.153   1959
  Planarity :  0.003   0.042   1601
  Dihedral  : 16.789 145.943   5341
  Min Nonbonded Distance : 1.298

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.35 (0.26), residues: 1007
  helix:  1.76 (0.24), residues: 487
  sheet:  1.10 (0.47), residues: 91
  loop : -0.10 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 400 
 TYR   0.009   0.001   TYR A 347 
 PHE   0.010   0.001   PHE A1276 
 TRP   0.005   0.001   TRP A 476 
 HIS   0.006   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.27 (12062)
  covalent geometry    : angle       0.55027 /  0.45 (16948)
  hydrogen bonds       : bond        0.15656 / 10.11 (  515)
  hydrogen bonds       : angle       5.65881 /  4.12 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 PHE cc_start: 0.8698 (m-80) cc_final: 0.8171 (m-10)
REVERT: A  549 VAL cc_start: 0.9213 (t) cc_final: 0.9001 (m)
REVERT: A  569 PHE cc_start: 0.9082 (m-80) cc_final: 0.8793 (m-10)
REVERT: A  587 PHE cc_start: 0.8104 (m-80) cc_final: 0.7646 (m-80)
REVERT: A  629 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8454 (mmm-85)
REVERT: A  964 SER cc_start: 0.9599 (t) cc_final: 0.9376 (p)
REVERT: A  981 TYR cc_start: 0.7725 (m-10) cc_final: 0.7198 (m-10)
REVERT: A 1164 LEU cc_start: 0.8497 (tp) cc_final: 0.8135 (tp)
REVERT: A 1352 ILE cc_start: 0.9141 (tt) cc_final: 0.8891 (tt)
REVERT: A 1357 GLU cc_start: 0.6695 (pt0) cc_final: 0.6109 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1236
  time to fit residues: 32.0090
Evaluate side-chains
  111 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:   30.0000
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:   40.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   overall best weight:    6.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  99 HIS
A 113 HIS
A 612 ASN
A 712 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.045270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.032983 restraints weight = 93632.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.034148 restraints weight = 50602.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.034928 restraints weight = 34149.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.035402 restraints weight = 26330.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.035770 restraints weight = 22271.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12062  Z= 0.229
  Angle     :  0.707  10.444  16948  Z= 0.388
  Chirality :  0.043   0.276   1959
  Planarity :  0.005   0.069   1601
  Dihedral  : 19.280 151.033   3176
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  8.42 %
    Favored  : 89.93 %
  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:  0.84 (0.26), residues: 1007
  helix:  1.25 (0.23), residues: 513
  sheet:  2.06 (0.53), residues: 69
  loop : -0.51 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 395 
 TYR   0.022   0.002   TYR A1141 
 PHE   0.017   0.002   PHE A 626 
 TRP   0.008   0.001   TRP A  18 
 HIS   0.010   0.002   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00443 /  0.23 (12062)
  covalent geometry    : angle       0.70740 /  0.39 (16948)
  hydrogen bonds       : bond        0.06346 /  4.09 (  515)
  hydrogen bonds       : angle       4.99910 /  3.66 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6848 (tmm) cc_final: 0.6624 (tmm)
REVERT: A   60 GLU cc_start: 0.9735 (pm20) cc_final: 0.9479 (pm20)
REVERT: A   86 PHE cc_start: 0.9771 (m-80) cc_final: 0.9129 (m-10)
REVERT: A  161 MET cc_start: 0.9390 (mmm) cc_final: 0.9145 (mmt)
REVERT: A  383 MET cc_start: 0.6648 (mtt) cc_final: 0.6277 (mtt)
REVERT: A  398 LEU cc_start: 0.9834 (tt) cc_final: 0.9375 (pp)
REVERT: A  569 PHE cc_start: 0.9372 (m-80) cc_final: 0.9146 (m-80)
REVERT: A  575 PHE cc_start: 0.8320 (m-10) cc_final: 0.8037 (m-80)
REVERT: A  587 PHE cc_start: 0.8571 (m-80) cc_final: 0.8285 (m-80)
REVERT: A  629 ARG cc_start: 0.9205 (mtt180) cc_final: 0.8500 (mmm-85)
REVERT: A  631 MET cc_start: 0.9335 (tpt) cc_final: 0.9099 (mmm)
REVERT: A  648 MET cc_start: 0.9479 (mmm) cc_final: 0.9266 (mmm)
REVERT: A  951 ARG cc_start: 0.9423 (mpp-170) cc_final: 0.9127 (mmt90)
REVERT: A 1089 MET cc_start: 0.8682 (mmm) cc_final: 0.7974 (mmm)
REVERT: A 1204 PHE cc_start: 0.9583 (m-10) cc_final: 0.9100 (m-10)
REVERT: A 1324 PHE cc_start: 0.7830 (p90) cc_final: 0.7350 (p90)
  outliers start: 15
  outliers final: 10
  residues processed: 115
  average time/residue: 0.1221
  time to fit residues: 19.2477
Evaluate side-chains
  87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  683 LEU
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1349 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 3 optimal weight:   30.0000
   chunk 55 optimal weight:   20.0000
   chunk 15 optimal weight:    3.9990
   chunk 43 optimal weight:   30.0000
   chunk 75 optimal weight:   20.0000
   chunk 41 optimal weight:    8.9990
   chunk 14 optimal weight:    3.9990
   chunk 87 optimal weight:    9.9990
   chunk 20 optimal weight:   10.0000
   chunk 42 optimal weight:    8.9990
   overall best weight:    6.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 309 ASN
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1101 GLN
A1297 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.043652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.031655 restraints weight = 96073.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.032767 restraints weight = 52798.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.033512 restraints weight = 35955.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.034022 restraints weight = 27831.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.034330 restraints weight = 23389.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12062  Z= 0.211
  Angle     :  0.621  10.739  16948  Z= 0.352
  Chirality :  0.040   0.203   1959
  Planarity :  0.004   0.063   1601
  Dihedral  : 19.426 154.815   3176
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.16 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.26), residues: 1007
  helix:  1.26 (0.22), residues: 507
  sheet:  1.97 (0.55), residues: 70
  loop : -0.77 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1303 
 TYR   0.027   0.002   TYR A1294 
 PHE   0.023   0.002   PHE A1204 
 TRP   0.007   0.001   TRP A 464 
 HIS   0.007   0.002   HIS A1297 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.21 (12062)
  covalent geometry    : angle       0.62050 /  0.35 (16948)
  hydrogen bonds       : bond        0.05658 /  3.62 (  515)
  hydrogen bonds       : angle       4.84945 /  3.56 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7077 (tmm) cc_final: 0.6760 (tmm)
REVERT: A   60 GLU cc_start: 0.9732 (pm20) cc_final: 0.9214 (pm20)
REVERT: A   86 PHE cc_start: 0.9791 (m-80) cc_final: 0.9183 (m-10)
REVERT: A  383 MET cc_start: 0.6858 (mtt) cc_final: 0.6519 (mtt)
REVERT: A  398 LEU cc_start: 0.9822 (tt) cc_final: 0.9222 (mt)
REVERT: A  575 PHE cc_start: 0.8443 (m-80) cc_final: 0.8184 (m-10)
REVERT: A  587 PHE cc_start: 0.8629 (m-80) cc_final: 0.8339 (m-80)
REVERT: A  629 ARG cc_start: 0.9158 (mtt180) cc_final: 0.8640 (mmt180)
REVERT: A  631 MET cc_start: 0.9392 (tpt) cc_final: 0.9070 (mmm)
REVERT: A  746 GLU cc_start: 0.9222 (mp0) cc_final: 0.8981 (mm-30)
REVERT: A  951 ARG cc_start: 0.9476 (mpp-170) cc_final: 0.9203 (mmt90)
REVERT: A 1226 LEU cc_start: 0.8638 (tp) cc_final: 0.8271 (mt)
REVERT: A 1271 GLU cc_start: 0.9620 (OUTLIER) cc_final: 0.9165 (pp20)
REVERT: A 1317 ASN cc_start: 0.8704 (m-40) cc_final: 0.8460 (m-40)
  outliers start: 17
  outliers final: 13
  residues processed: 96
  average time/residue: 0.1089
  time to fit residues: 14.9915
Evaluate side-chains
  89 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  694 MET
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1271 GLU
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1337 THR
Chi-restraints excluded: chain A residue 1349 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 82 optimal weight:    2.9990
   chunk 97 optimal weight:    8.9990
   chunk 44 optimal weight:    0.0470
   chunk 48 optimal weight:    8.9990
   chunk 90 optimal weight:    8.9990
   chunk 68 optimal weight:    8.9990
   chunk 49 optimal weight:    0.4980
   chunk 2 optimal weight:    0.0870
   chunk 8 optimal weight:    6.9990
   chunk 105 optimal weight:   40.0000
   overall best weight:    2.1260

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.044131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.032154 restraints weight = 92565.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.033266 restraints weight = 50660.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.034027 restraints weight = 34303.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.034510 restraints weight = 26385.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.034869 restraints weight = 22171.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  12062  Z= 0.132
  Angle     :  0.574  11.907  16948  Z= 0.321
  Chirality :  0.040   0.254   1959
  Planarity :  0.004   0.061   1601
  Dihedral  : 19.467 156.200   3176
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.83 %
    Favored  : 87.42 %
  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:  0.85 (0.26), residues: 1007
  helix:  1.44 (0.23), residues: 508
  sheet:  2.05 (0.56), residues: 70
  loop : -0.77 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  63 
 TYR   0.013   0.001   TYR A1294 
 PHE   0.013   0.001   PHE A1276 
 TRP   0.004   0.000   TRP A 476 
 HIS   0.005   0.001   HIS A1349 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.13 (12062)
  covalent geometry    : angle       0.57380 /  0.32 (16948)
  hydrogen bonds       : bond        0.04737 /  2.96 (  515)
  hydrogen bonds       : angle       4.55336 /  3.35 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7095 (tmm) cc_final: 0.6752 (tmm)
REVERT: A   60 GLU cc_start: 0.9622 (pm20) cc_final: 0.9373 (pm20)
REVERT: A   86 PHE cc_start: 0.9757 (m-80) cc_final: 0.9117 (m-10)
REVERT: A  370 GLU cc_start: 0.9379 (pm20) cc_final: 0.8955 (pm20)
REVERT: A  383 MET cc_start: 0.6804 (mtt) cc_final: 0.6459 (mtt)
REVERT: A  495 MET cc_start: 0.8939 (mpp) cc_final: 0.8694 (pmm)
REVERT: A  524 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9182 (pp)
REVERT: A  587 PHE cc_start: 0.8604 (m-80) cc_final: 0.8330 (m-80)
REVERT: A  629 ARG cc_start: 0.9133 (mtt180) cc_final: 0.8714 (mmt90)
REVERT: A  631 MET cc_start: 0.9397 (tpt) cc_final: 0.9104 (mmm)
REVERT: A  648 MET cc_start: 0.9404 (mmm) cc_final: 0.9171 (mmm)
REVERT: A  652 LYS cc_start: 0.9439 (tttt) cc_final: 0.8874 (ttpp)
REVERT: A  746 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8908 (mm-30)
REVERT: A  949 LEU cc_start: 0.9278 (mt) cc_final: 0.9075 (mt)
REVERT: A  951 ARG cc_start: 0.9466 (mpp-170) cc_final: 0.9132 (mmt90)
REVERT: A  977 GLU cc_start: 0.8325 (mp0) cc_final: 0.7980 (pm20)
REVERT: A 1089 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7145 (mmm)
REVERT: A 1096 LYS cc_start: 0.9034 (tptt) cc_final: 0.8511 (ttmm)
  outliers start: 16
  outliers final: 9
  residues processed: 93
  average time/residue: 0.0876
  time to fit residues: 11.9716
Evaluate side-chains
  87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue 1089 MET
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1324 PHE
Chi-restraints excluded: chain A residue 1349 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 16 optimal weight:   20.0000
   chunk 99 optimal weight:   20.0000
   chunk 102 optimal weight:   40.0000
   chunk 107 optimal weight:   30.0000
   chunk 31 optimal weight:    7.9990
   chunk 36 optimal weight:    9.9990
   chunk 78 optimal weight:   20.0000
   chunk 75 optimal weight:   10.0000
   chunk 98 optimal weight:    8.9990
   chunk 105 optimal weight:   40.0000
   overall best weight:    9.3994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 511 HIS
A 739 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.040069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.028855 restraints weight = 101293.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.029802 restraints weight = 56252.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.030448 restraints weight = 38568.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.030899 restraints weight = 30198.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.031229 restraints weight = 25449.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.4745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  12062  Z= 0.308
  Angle     :  0.779  13.001  16948  Z= 0.424
  Chirality :  0.044   0.200   1959
  Planarity :  0.006   0.068   1601
  Dihedral  : 19.830 159.737   3176
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 19.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 10.39 %
    Favored  : 86.32 %
  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: -0.00 (0.25), residues: 1007
  helix:  0.79 (0.22), residues: 516
  sheet:  1.35 (0.57), residues: 68
  loop : -1.22 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 152 
 TYR   0.016   0.003   TYR A1237 
 PHE   0.022   0.003   PHE A1324 
 TRP   0.013   0.002   TRP A 659 
 HIS   0.011   0.003   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00573 /  0.31 (12062)
  covalent geometry    : angle       0.77893 /  0.42 (16948)
  hydrogen bonds       : bond        0.07685 /  5.21 (  515)
  hydrogen bonds       : angle       5.01967 /  3.69 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 71
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7299 (tmm) cc_final: 0.6918 (tmm)
REVERT: A   60 GLU cc_start: 0.9651 (pm20) cc_final: 0.9422 (pm20)
REVERT: A  161 MET cc_start: 0.9407 (mmt) cc_final: 0.9023 (mmm)
REVERT: A  321 MET cc_start: 0.9761 (mmp) cc_final: 0.9368 (mmp)
REVERT: A  383 MET cc_start: 0.7098 (mtt) cc_final: 0.6694 (mtt)
REVERT: A  629 ARG cc_start: 0.9209 (mtt180) cc_final: 0.8814 (mmt90)
REVERT: A  631 MET cc_start: 0.9414 (tpt) cc_final: 0.8993 (mmm)
REVERT: A  648 MET cc_start: 0.9556 (mmm) cc_final: 0.9319 (mmm)
REVERT: A  652 LYS cc_start: 0.9502 (tttt) cc_final: 0.8887 (ttpp)
REVERT: A  746 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8945 (mm-30)
REVERT: A  951 ARG cc_start: 0.9507 (mpp-170) cc_final: 0.9177 (mmt90)
REVERT: A 1096 LYS cc_start: 0.9155 (tptt) cc_final: 0.8647 (ttmm)
  outliers start: 30
  outliers final: 24
  residues processed: 92
  average time/residue: 0.0944
  time to fit residues: 12.6967
Evaluate side-chains
  90 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  645 ASP
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  694 MET
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue  751 MET
Chi-restraints excluded: chain A residue 1125 ASP
Chi-restraints excluded: chain A residue 1192 LYS
Chi-restraints excluded: chain A residue 1226 LEU
Chi-restraints excluded: chain A residue 1260 GLU
Chi-restraints excluded: chain A residue 1271 GLU
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1337 THR
Chi-restraints excluded: chain A residue 1349 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 65 optimal weight:    7.9990
   chunk 99 optimal weight:   20.0000
   chunk 23 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 45 optimal weight:   30.0000
   chunk 98 optimal weight:    5.9990
   chunk 109 optimal weight:   40.0000
   chunk 26 optimal weight:    0.9990
   chunk 97 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    5.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 402 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.040762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.029219 restraints weight = 98511.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.030243 restraints weight = 54514.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.030938 restraints weight = 37396.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.031354 restraints weight = 29044.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.031691 restraints weight = 24753.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.4894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12062  Z= 0.175
  Angle     :  0.603  12.136  16948  Z= 0.339
  Chirality :  0.040   0.240   1959
  Planarity :  0.004   0.066   1601
  Dihedral  : 19.808 160.449   3176
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.14 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.26), residues: 1007
  helix:  1.01 (0.22), residues: 521
  sheet:  1.33 (0.56), residues: 68
  loop : -0.97 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1171 
 TYR   0.012   0.001   TYR A1242 
 PHE   0.020   0.002   PHE A1181 
 TRP   0.008   0.001   TRP A 464 
 HIS   0.004   0.001   HIS A 930 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.18 (12062)
  covalent geometry    : angle       0.60341 /  0.34 (16948)
  hydrogen bonds       : bond        0.05031 /  3.19 (  515)
  hydrogen bonds       : angle       4.72147 /  3.47 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7410 (tmm) cc_final: 0.7039 (tmm)
REVERT: A   60 GLU cc_start: 0.9637 (pm20) cc_final: 0.9381 (pm20)
REVERT: A  161 MET cc_start: 0.9476 (mmt) cc_final: 0.9082 (mmm)
REVERT: A  524 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9227 (pp)
REVERT: A  587 PHE cc_start: 0.8389 (m-10) cc_final: 0.7792 (m-10)
REVERT: A  631 MET cc_start: 0.9445 (tpt) cc_final: 0.9081 (mmm)
REVERT: A  648 MET cc_start: 0.9600 (mmm) cc_final: 0.9356 (mmm)
REVERT: A  652 LYS cc_start: 0.9462 (tttt) cc_final: 0.9248 (ttpp)
REVERT: A  746 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8908 (mm-30)
REVERT: A  949 LEU cc_start: 0.9268 (mt) cc_final: 0.9042 (mm)
REVERT: A  951 ARG cc_start: 0.9511 (mpp-170) cc_final: 0.9154 (mmt90)
REVERT: A 1198 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9245 (mm)
  outliers start: 21
  outliers final: 14
  residues processed: 82
  average time/residue: 0.1072
  time to fit residues: 12.6898
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue 1192 LYS
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1226 LEU
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1349 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 75 optimal weight:   20.0000
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 90 optimal weight:    0.1980
   chunk 68 optimal weight:    8.9990
   chunk 52 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    4.4388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.040725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.029354 restraints weight = 100663.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.030390 restraints weight = 54171.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.031102 restraints weight = 36504.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.031531 restraints weight = 28122.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.031879 restraints weight = 23849.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.5137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12062  Z= 0.161
  Angle     :  0.618  19.757  16948  Z= 0.334
  Chirality :  0.040   0.304   1959
  Planarity :  0.004   0.063   1601
  Dihedral  : 19.807 161.031   3176
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.14 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.26), residues: 1007
  helix:  1.09 (0.22), residues: 521
  sheet:  1.19 (0.55), residues: 68
  loop : -0.97 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 671 
 TYR   0.012   0.001   TYR A1237 
 PHE   0.019   0.002   PHE A1105 
 TRP   0.004   0.001   TRP A 464 
 HIS   0.005   0.001   HIS A 930 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.16 (12062)
  covalent geometry    : angle       0.61806 /  0.33 (16948)
  hydrogen bonds       : bond        0.04980 /  3.16 (  515)
  hydrogen bonds       : angle       4.67416 /  3.42 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7348 (tmm) cc_final: 0.6972 (tmm)
REVERT: A   60 GLU cc_start: 0.9641 (pm20) cc_final: 0.9393 (pm20)
REVERT: A  161 MET cc_start: 0.9459 (mmt) cc_final: 0.9060 (mmm)
REVERT: A  524 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9199 (pp)
REVERT: A  629 ARG cc_start: 0.9253 (mtt180) cc_final: 0.8722 (mmm-85)
REVERT: A  648 MET cc_start: 0.9630 (mmm) cc_final: 0.9387 (mmm)
REVERT: A  652 LYS cc_start: 0.9496 (tttt) cc_final: 0.8792 (ttpp)
REVERT: A  746 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8947 (mm-30)
REVERT: A  949 LEU cc_start: 0.9236 (mt) cc_final: 0.9002 (mm)
REVERT: A  951 ARG cc_start: 0.9512 (mpp-170) cc_final: 0.9191 (mmt90)
REVERT: A 1096 LYS cc_start: 0.9025 (tptt) cc_final: 0.8546 (ttmm)
REVERT: A 1198 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9208 (mm)
  outliers start: 21
  outliers final: 15
  residues processed: 81
  average time/residue: 0.1079
  time to fit residues: 12.6531
Evaluate side-chains
  78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue 1192 LYS
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1226 LEU
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1349 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 97 optimal weight:    8.9990
   chunk 74 optimal weight:   20.0000
   chunk 68 optimal weight:    5.9990
   chunk 102 optimal weight:   40.0000
   chunk 43 optimal weight:    4.9990
   chunk 27 optimal weight:    9.9990
   chunk 78 optimal weight:   20.0000
   chunk 103 optimal weight:   30.0000
   chunk 3 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    7.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.039072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.028110 restraints weight = 104827.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.029082 restraints weight = 57647.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.029745 restraints weight = 39483.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.030138 restraints weight = 30730.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.030459 restraints weight = 26261.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.5792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12062  Z= 0.239
  Angle     :  0.669  13.555  16948  Z= 0.370
  Chirality :  0.042   0.326   1959
  Planarity :  0.005   0.060   1601
  Dihedral  : 20.003 162.254   3176
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 17.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 12.25 %
    Favored  : 85.01 %
  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:  0.00 (0.25), residues: 1007
  helix:  0.80 (0.22), residues: 523
  sheet:  0.90 (0.56), residues: 68
  loop : -1.16 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 671 
 TYR   0.013   0.002   TYR A 568 
 PHE   0.025   0.002   PHE A 587 
 TRP   0.013   0.002   TRP A 464 
 HIS   0.007   0.002   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00440 /  0.24 (12062)
  covalent geometry    : angle       0.66942 /  0.37 (16948)
  hydrogen bonds       : bond        0.06049 /  3.96 (  515)
  hydrogen bonds       : angle       4.89301 /  3.56 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 60
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7479 (tmm) cc_final: 0.7042 (tmm)
REVERT: A   60 GLU cc_start: 0.9586 (pm20) cc_final: 0.9338 (pm20)
REVERT: A  161 MET cc_start: 0.9222 (mmt) cc_final: 0.8925 (mmm)
REVERT: A  321 MET cc_start: 0.9642 (mmp) cc_final: 0.9250 (mmp)
REVERT: A  495 MET cc_start: 0.9062 (pmm) cc_final: 0.8624 (pmm)
REVERT: A  524 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9234 (pp)
REVERT: A  629 ARG cc_start: 0.9319 (mtt180) cc_final: 0.8831 (mmt90)
REVERT: A  631 MET cc_start: 0.9349 (tpt) cc_final: 0.9023 (mmm)
REVERT: A  746 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8836 (mm-30)
REVERT: A  949 LEU cc_start: 0.9258 (mt) cc_final: 0.8985 (mt)
REVERT: A  951 ARG cc_start: 0.9475 (mpp-170) cc_final: 0.9165 (mmt90)
REVERT: A 1089 MET cc_start: 0.8825 (mmt) cc_final: 0.8569 (tpt)
REVERT: A 1096 LYS cc_start: 0.9267 (tptt) cc_final: 0.8729 (ttmm)
REVERT: A 1198 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9265 (mm)
  outliers start: 25
  outliers final: 17
  residues processed: 78
  average time/residue: 0.1042
  time to fit residues: 11.6089
Evaluate side-chains
  80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 60
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  575 PHE
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  694 MET
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue 1192 LYS
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1226 LEU
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1349 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 86 optimal weight:    9.9990
   chunk 83 optimal weight:    1.9990
   chunk 64 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 4 optimal weight:   20.0000
   chunk 55 optimal weight:    6.9990
   chunk 111 optimal weight:   30.0000
   chunk 78 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 46 optimal weight:   20.0000
   overall best weight:    6.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 595 HIS
** A 985 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 = 0.3020 r_free = 0.3020 target = 0.038813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.027944 restraints weight = 103057.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.028922 restraints weight = 56731.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.029567 restraints weight = 38833.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.029973 restraints weight = 30278.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.030276 restraints weight = 25766.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.6079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12062  Z= 0.205
  Angle     :  0.646  15.219  16948  Z= 0.353
  Chirality :  0.040   0.210   1959
  Planarity :  0.004   0.058   1601
  Dihedral  : 20.036 161.576   3176
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.35 %
    Favored  : 84.46 %
  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:  0.03 (0.26), residues: 1007
  helix:  0.83 (0.22), residues: 523
  sheet:  0.88 (0.64), residues: 58
  loop : -1.10 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1171 
 TYR   0.012   0.002   TYR A 568 
 PHE   0.025   0.002   PHE A1105 
 TRP   0.010   0.001   TRP A 464 
 HIS   0.005   0.001   HIS A 930 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.20 (12062)
  covalent geometry    : angle       0.64569 /  0.35 (16948)
  hydrogen bonds       : bond        0.05300 /  3.39 (  515)
  hydrogen bonds       : angle       4.85502 /  3.53 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7583 (tmm) cc_final: 0.7208 (tmm)
REVERT: A   60 GLU cc_start: 0.9649 (pm20) cc_final: 0.9394 (pm20)
REVERT: A  125 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8204 (mm-30)
REVERT: A  161 MET cc_start: 0.9475 (mmt) cc_final: 0.9129 (mmm)
REVERT: A  383 MET cc_start: 0.7637 (mtt) cc_final: 0.7246 (ttt)
REVERT: A  495 MET cc_start: 0.8856 (pmm) cc_final: 0.8602 (pmm)
REVERT: A  524 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9226 (pp)
REVERT: A  629 ARG cc_start: 0.9292 (mtt180) cc_final: 0.8866 (mmt180)
REVERT: A  631 MET cc_start: 0.9426 (tpt) cc_final: 0.9069 (mmm)
REVERT: A  746 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8901 (mm-30)
REVERT: A 1089 MET cc_start: 0.8687 (mmt) cc_final: 0.8434 (tpt)
REVERT: A 1198 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9120 (mm)
  outliers start: 20
  outliers final: 14
  residues processed: 77
  average time/residue: 0.1016
  time to fit residues: 11.1155
Evaluate side-chains
  76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1192 LYS
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1226 LEU
Chi-restraints excluded: chain A residue 1302 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 95 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 37 optimal weight:   10.0000
   chunk 86 optimal weight:    7.9990
   chunk 57 optimal weight:    0.0770
   chunk 2 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 54 optimal weight:    7.9990
   chunk 71 optimal weight:   30.0000
   chunk 38 optimal weight:   10.0000
   overall best weight:    5.6146

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 723 HIS
** A 985 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 = 0.3018 r_free = 0.3018 target = 0.038720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.027835 restraints weight = 104760.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.028810 restraints weight = 57160.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.029464 restraints weight = 39124.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.029909 restraints weight = 30466.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.030165 restraints weight = 25751.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.6315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12062  Z= 0.182
  Angle     :  0.646  14.661  16948  Z= 0.348
  Chirality :  0.040   0.207   1959
  Planarity :  0.004   0.055   1601
  Dihedral  : 20.027 161.836   3176
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.11 %
    Favored  : 83.81 %
  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:  0.16 (0.26), residues: 1007
  helix:  0.95 (0.22), residues: 522
  sheet:  0.68 (0.60), residues: 68
  loop : -1.06 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 494 
 TYR   0.011   0.001   TYR A 568 
 PHE   0.019   0.002   PHE A1105 
 TRP   0.009   0.001   TRP A 464 
 HIS   0.005   0.001   HIS A 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.18 (12062)
  covalent geometry    : angle       0.64640 /  0.35 (16948)
  hydrogen bonds       : bond        0.05210 /  3.33 (  515)
  hydrogen bonds       : angle       4.74938 /  3.46 ( 1368)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7640 (tmm) cc_final: 0.7253 (tmm)
REVERT: A   60 GLU cc_start: 0.9631 (pm20) cc_final: 0.9367 (pm20)
REVERT: A  125 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8187 (mm-30)
REVERT: A  161 MET cc_start: 0.9403 (mmt) cc_final: 0.9074 (mmm)
REVERT: A  321 MET cc_start: 0.9686 (mmp) cc_final: 0.9321 (mmp)
REVERT: A  383 MET cc_start: 0.7633 (mtt) cc_final: 0.7277 (ttt)
REVERT: A  495 MET cc_start: 0.8952 (pmm) cc_final: 0.8649 (pmm)
REVERT: A  524 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9236 (pp)
REVERT: A  629 ARG cc_start: 0.9324 (mtt180) cc_final: 0.8855 (mmt180)
REVERT: A  746 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8871 (mm-30)
REVERT: A  943 TYR cc_start: 0.9626 (OUTLIER) cc_final: 0.9419 (t80)
REVERT: A  949 LEU cc_start: 0.9123 (mt) cc_final: 0.8769 (mm)
REVERT: A  951 ARG cc_start: 0.9537 (mtm-85) cc_final: 0.9247 (mmt-90)
REVERT: A 1089 MET cc_start: 0.8856 (mmt) cc_final: 0.8608 (tpt)
REVERT: A 1198 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9161 (mm)
  outliers start: 19
  outliers final: 13
  residues processed: 75
  average time/residue: 0.1061
  time to fit residues: 11.5412
Evaluate side-chains
  76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  364 ASP
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  694 MET
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain A residue 1192 LYS
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1226 LEU
Chi-restraints excluded: chain A residue 1302 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 79 optimal weight:    7.9990
   chunk 50 optimal weight:   20.0000
   chunk 75 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 23 optimal weight:    8.9990
   chunk 7 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 43 optimal weight:   20.0000
   chunk 20 optimal weight:    9.9990
   overall best weight:    7.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 985 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 = 0.2998 r_free = 0.2998 target = 0.037668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.027013 restraints weight = 106154.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.027970 restraints weight = 57781.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.028605 restraints weight = 39350.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.028985 restraints weight = 30493.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.029287 restraints weight = 25976.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.6863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12062  Z= 0.231
  Angle     :  0.689  14.363  16948  Z= 0.373
  Chirality :  0.041   0.201   1959
  Planarity :  0.005   0.055   1601
  Dihedral  : 20.159 162.184   3176
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 17.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.33 %
    Favored  : 83.59 %
  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: -0.16 (0.26), residues: 1007
  helix:  0.70 (0.22), residues: 520
  sheet:  0.38 (0.60), residues: 69
  loop : -1.17 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1212 
 TYR   0.020   0.002   TYR A1356 
 PHE   0.047   0.002   PHE A1204 
 TRP   0.016   0.002   TRP A 464 
 HIS   0.006   0.002   HIS A 982 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00430 /  0.23 (12062)
  covalent geometry    : angle       0.68866 /  0.37 (16948)
  hydrogen bonds       : bond        0.06067 /  3.98 (  515)
  hydrogen bonds       : angle       4.98886 /  3.62 ( 1368)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1769.93 seconds
wall clock time: 31 minutes 31.54 seconds (1891.54 seconds total)