Starting phenix.real_space_refine
on Wed Aug  5 20:53:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k4c_62054/08_2026/9k4c_62054.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k4c_62054/08_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_62054/08_2026/9k4c_62054.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k4c_62054/08_2026/9k4c_62054.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k4c_62054/08_2026/9k4c_62054.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k4c_62054/08_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-2.2rc3-6140/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: 2.46, per 1000 atoms: 0.21
  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: 0.73
  Conformation dependent library (CDL) restraints added in 392.6 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: 1.27
  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: 2.08

  Time building geometry restraints manager: 0.98 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: 15849
        1.21 -     2.43: 893
        2.43 -     3.64: 196
        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 -    0.033: 1289
       0.033 -    0.066: 400
       0.066 -    0.100: 137
       0.100 -    0.133: 81
       0.133 -    0.166: 52
  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      2.47    2.30    0.17 2.00e-01 2.50e+01 6.90e-01
  chirality pdb=" C2'   G D  35 "
            pdb=" C3'   G D  35 "
            pdb=" O2'   G D  35 "
            pdb=" C1'   G D  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.77    0.15 2.00e-01 2.50e+01 5.45e-01
  chirality pdb=" C2'   C D  13 "
            pdb=" C3'   C D  13 "
            pdb=" O2'   C D  13 "
            pdb=" C1'   C D  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.76    0.15 2.00e-01 2.50e+01 5.35e-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:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.480
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.390
-------------------------------------------------------------------------------
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= 0.272
  Angle     :  0.631   6.069  16948  Z= 0.510
  Chirality :  0.047   0.166   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        0.00312 /  0.27 (12062)
  covalent geometry    : angle       0.63140 /  0.51 (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  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 PHE cc_start: 0.8698 (m-80) cc_final: 0.8172 (m-10)
REVERT: A  549 VAL cc_start: 0.9213 (t) cc_final: 0.9002 (m)
REVERT: A  569 PHE cc_start: 0.9082 (m-80) cc_final: 0.8792 (m-10)
REVERT: A  587 PHE cc_start: 0.8104 (m-80) cc_final: 0.7647 (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: 0.7199 (m-10)
REVERT: A 1164 LEU cc_start: 0.8497 (tp) cc_final: 0.8136 (tp)
REVERT: A 1352 ILE cc_start: 0.9141 (tt) cc_final: 0.8890 (tt)
REVERT: A 1357 GLU cc_start: 0.6695 (pt0) cc_final: 0.6105 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1058
  time to fit residues: 27.3197
Evaluate side-chains
  109 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
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:   40.0000
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:   50.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:   20.0000
   overall best weight:    7.3990

-------------------------------------------------------------------------------
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 = 0.3163 r_free = 0.3163 target = 0.044646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.032352 restraints weight = 94101.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.033496 restraints weight = 51645.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.034255 restraints weight = 35245.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.034721 restraints weight = 27391.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.035092 restraints weight = 23270.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12062  Z= 0.246
  Angle     :  0.742  10.505  16948  Z= 0.403
  Chirality :  0.044   0.249   1959
  Planarity :  0.005   0.070   1601
  Dihedral  : 19.275 149.713   3176
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  8.75 %
    Favored  : 89.50 %
  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:  0.77 (0.26), residues: 1007
  helix:  1.19 (0.23), residues: 513
  sheet:  2.03 (0.53), residues: 69
  loop : -0.55 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 691 
 TYR   0.024   0.002   TYR A1141 
 PHE   0.020   0.002   PHE A 626 
 TRP   0.007   0.002   TRP A 476 
 HIS   0.010   0.002   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00463 /  0.25 (12062)
  covalent geometry    : angle       0.74199 /  0.40 (16948)
  hydrogen bonds       : bond        0.06659 /  4.27 (  515)
  hydrogen bonds       : angle       5.04622 /  3.69 ( 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
  112 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6897 (tmm) cc_final: 0.6657 (tmm)
REVERT: A   60 GLU cc_start: 0.9617 (pm20) cc_final: 0.9404 (pm20)
REVERT: A   86 PHE cc_start: 0.9780 (m-80) cc_final: 0.9130 (m-10)
REVERT: A  161 MET cc_start: 0.9406 (mmm) cc_final: 0.9151 (mmt)
REVERT: A  321 MET cc_start: 0.9758 (mmm) cc_final: 0.9557 (mmm)
REVERT: A  383 MET cc_start: 0.6748 (mtt) cc_final: 0.6431 (mtt)
REVERT: A  398 LEU cc_start: 0.9841 (tt) cc_final: 0.9401 (pp)
REVERT: A  569 PHE cc_start: 0.9378 (m-80) cc_final: 0.9146 (m-80)
REVERT: A  575 PHE cc_start: 0.8359 (m-10) cc_final: 0.8070 (m-80)
REVERT: A  587 PHE cc_start: 0.8654 (m-80) cc_final: 0.8298 (m-80)
REVERT: A  629 ARG cc_start: 0.9206 (mtt180) cc_final: 0.8531 (mmm-85)
REVERT: A  631 MET cc_start: 0.9344 (tpt) cc_final: 0.9066 (mmm)
REVERT: A  648 MET cc_start: 0.9519 (mmm) cc_final: 0.9315 (mmm)
REVERT: A  943 TYR cc_start: 0.9571 (m-80) cc_final: 0.9369 (m-80)
REVERT: A  951 ARG cc_start: 0.9429 (mpp-170) cc_final: 0.9164 (mmt90)
REVERT: A 1089 MET cc_start: 0.8642 (mmm) cc_final: 0.7866 (mmm)
REVERT: A 1204 PHE cc_start: 0.9585 (m-10) cc_final: 0.9091 (m-10)
REVERT: A 1324 PHE cc_start: 0.7915 (p90) cc_final: 0.7440 (p90)
  outliers start: 16
  outliers final: 12
  residues processed: 111
  average time/residue: 0.1036
  time to fit residues: 15.9576
Evaluate side-chains
  88 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
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  507 VAL
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 1302 ILE
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:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 55 optimal weight:   20.0000
   chunk 15 optimal weight:    7.9990
   chunk 43 optimal weight:   30.0000
   chunk 75 optimal weight:   20.0000
   chunk 41 optimal weight:   30.0000
   chunk 14 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    7.7992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 309 ASN
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 511 HIS
A1101 GLN
A1297 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.042220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.030526 restraints weight = 98531.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.031588 restraints weight = 54240.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.032265 restraints weight = 37001.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.032773 restraints weight = 28860.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.033064 restraints weight = 24331.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12062  Z= 0.244
  Angle     :  0.684  15.379  16948  Z= 0.383
  Chirality :  0.043   0.263   1959
  Planarity :  0.005   0.055   1601
  Dihedral  : 19.477 154.803   3176
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 10.94 %
    Favored  : 86.54 %
  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:  0.47 (0.25), residues: 1007
  helix:  1.13 (0.22), residues: 507
  sheet:  1.74 (0.55), residues: 68
  loop : -0.90 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  63 
 TYR   0.018   0.002   TYR A 943 
 PHE   0.039   0.003   PHE A1204 
 TRP   0.011   0.001   TRP A 464 
 HIS   0.007   0.002   HIS A 723 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00458 /  0.24 (12062)
  covalent geometry    : angle       0.68445 /  0.38 (16948)
  hydrogen bonds       : bond        0.05944 /  3.89 (  515)
  hydrogen bonds       : angle       4.96273 /  3.64 ( 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
  100 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 77
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7106 (tmm) cc_final: 0.6774 (tmm)
REVERT: A   60 GLU cc_start: 0.9600 (pm20) cc_final: 0.9366 (pm20)
REVERT: A  383 MET cc_start: 0.7021 (mtt) cc_final: 0.6672 (mtt)
REVERT: A  398 LEU cc_start: 0.9822 (OUTLIER) cc_final: 0.9116 (mt)
REVERT: A  495 MET cc_start: 0.9338 (mpp) cc_final: 0.8778 (pmm)
REVERT: A  575 PHE cc_start: 0.8494 (m-80) cc_final: 0.8246 (m-80)
REVERT: A  587 PHE cc_start: 0.8772 (m-80) cc_final: 0.8568 (m-80)
REVERT: A  629 ARG cc_start: 0.9202 (mtt180) cc_final: 0.8614 (mmm-85)
REVERT: A  631 MET cc_start: 0.9390 (tpt) cc_final: 0.9103 (mmm)
REVERT: A  746 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8963 (mm-30)
REVERT: A  951 ARG cc_start: 0.9500 (mpp-170) cc_final: 0.9203 (mmt90)
REVERT: A 1226 LEU cc_start: 0.8784 (tp) cc_final: 0.8471 (mt)
REVERT: A 1271 GLU cc_start: 0.9615 (OUTLIER) cc_final: 0.9260 (pp20)
  outliers start: 23
  outliers final: 16
  residues processed: 94
  average time/residue: 0.0893
  time to fit residues: 12.1719
Evaluate side-chains
  91 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
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  398 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  680 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 1139 VAL
Chi-restraints excluded: chain A residue 1192 LYS
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:   20.0000
   chunk 82 optimal weight:    8.9990
   chunk 97 optimal weight:    8.9990
   chunk 44 optimal weight:   20.0000
   chunk 48 optimal weight:    9.9990
   chunk 90 optimal weight:    0.4980
   chunk 68 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 105 optimal weight:   50.0000
   overall best weight:    5.4988

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.041936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.030265 restraints weight = 98897.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.031286 restraints weight = 54901.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.031981 restraints weight = 37879.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.032408 restraints weight = 29537.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.032750 restraints weight = 25232.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.4227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12062  Z= 0.188
  Angle     :  0.597  11.162  16948  Z= 0.338
  Chirality :  0.040   0.222   1959
  Planarity :  0.004   0.054   1601
  Dihedral  : 19.576 155.301   3176
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.14 %
    Favored  : 86.11 %
  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:  0.56 (0.26), residues: 1007
  helix:  1.24 (0.22), residues: 516
  sheet:  1.74 (0.58), residues: 68
  loop : -0.95 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 951 
 TYR   0.011   0.001   TYR A1242 
 PHE   0.015   0.002   PHE A1324 
 TRP   0.007   0.001   TRP A 464 
 HIS   0.006   0.001   HIS A 930 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.19 (12062)
  covalent geometry    : angle       0.59650 /  0.34 (16948)
  hydrogen bonds       : bond        0.05187 /  3.32 (  515)
  hydrogen bonds       : angle       4.75996 /  3.48 ( 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
  86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.285 
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: 0.7138 (tmm) cc_final: 0.6805 (tmm)
REVERT: A   60 GLU cc_start: 0.9598 (pm20) cc_final: 0.9317 (pm20)
REVERT: A  161 MET cc_start: 0.9495 (mmt) cc_final: 0.9269 (mmt)
REVERT: A  398 LEU cc_start: 0.9797 (tt) cc_final: 0.9226 (mt)
REVERT: A  524 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9169 (pp)
REVERT: A  629 ARG cc_start: 0.9225 (mtt180) cc_final: 0.8698 (mmt-90)
REVERT: A  631 MET cc_start: 0.9420 (tpt) cc_final: 0.9103 (mmm)
REVERT: A  746 GLU cc_start: 0.9234 (mp0) cc_final: 0.8981 (mm-30)
REVERT: A  951 ARG cc_start: 0.9512 (mpp-170) cc_final: 0.9146 (mmt90)
REVERT: A 1125 ASP cc_start: 0.9598 (OUTLIER) cc_final: 0.9364 (p0)
  outliers start: 16
  outliers final: 10
  residues processed: 81
  average time/residue: 0.0815
  time to fit residues: 9.9041
Evaluate side-chains
  77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  364 ASP
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  680 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue 1125 ASP
Chi-restraints excluded: chain A residue 1302 ILE
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:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 99 optimal weight:    6.9990
   chunk 102 optimal weight:   40.0000
   chunk 107 optimal weight:   30.0000
   chunk 31 optimal weight:    0.9990
   chunk 36 optimal weight:    9.9990
   chunk 78 optimal weight:   20.0000
   chunk 75 optimal weight:    8.9990
   chunk 98 optimal weight:    9.9990
   chunk 105 optimal weight:   50.0000
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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 = 0.3091 r_free = 0.3091 target = 0.040585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.029299 restraints weight = 99749.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.030332 restraints weight = 53959.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.031014 restraints weight = 36511.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.031465 restraints weight = 28316.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.031774 restraints weight = 23891.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.4916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  12062  Z= 0.218
  Angle     :  0.641  13.740  16948  Z= 0.354
  Chirality :  0.041   0.223   1959
  Planarity :  0.004   0.058   1601
  Dihedral  : 19.731 158.518   3176
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 12.04 %
    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:  0.34 (0.26), residues: 1007
  helix:  1.09 (0.22), residues: 517
  sheet:  1.33 (0.57), residues: 66
  loop : -1.03 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  63 
 TYR   0.014   0.002   TYR A1356 
 PHE   0.024   0.002   PHE A1105 
 TRP   0.006   0.001   TRP A 464 
 HIS   0.006   0.002   HIS A 930 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00402 /  0.22 (12062)
  covalent geometry    : angle       0.64143 /  0.35 (16948)
  hydrogen bonds       : bond        0.05654 /  3.69 (  515)
  hydrogen bonds       : angle       4.78779 /  3.51 ( 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
  94 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 67
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7307 (tmm) cc_final: 0.6939 (tmm)
REVERT: A   60 GLU cc_start: 0.9619 (pm20) cc_final: 0.9335 (pm20)
REVERT: A  321 MET cc_start: 0.9722 (mmp) cc_final: 0.9471 (mmp)
REVERT: A  524 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9187 (pp)
REVERT: A  629 ARG cc_start: 0.9273 (mtt180) cc_final: 0.8777 (mmt-90)
REVERT: A  631 MET cc_start: 0.9416 (tpt) cc_final: 0.9104 (mmm)
REVERT: A  746 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8932 (mm-30)
REVERT: A  951 ARG cc_start: 0.9537 (mpp-170) cc_final: 0.9190 (mmt90)
REVERT: A 1096 LYS cc_start: 0.9058 (tptt) cc_final: 0.8572 (ttmm)
  outliers start: 27
  outliers final: 20
  residues processed: 89
  average time/residue: 0.0824
  time to fit residues: 11.0795
Evaluate side-chains
  85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 VAL
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  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  680 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 1226 LEU
Chi-restraints excluded: chain A residue 1260 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:    6.9990
   chunk 99 optimal weight:   20.0000
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 45 optimal weight:    9.9990
   chunk 98 optimal weight:    7.9990
   chunk 109 optimal weight:   50.0000
   chunk 26 optimal weight:    7.9990
   chunk 97 optimal weight:    0.4980
   chunk 11 optimal weight:    4.9990
   overall best weight:    4.0988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 739 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.040969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.029602 restraints weight = 98923.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.030648 restraints weight = 52860.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.031357 restraints weight = 35544.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.031802 restraints weight = 27383.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.032138 restraints weight = 23104.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.5051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12062  Z= 0.150
  Angle     :  0.571  11.621  16948  Z= 0.320
  Chirality :  0.039   0.217   1959
  Planarity :  0.003   0.054   1601
  Dihedral  : 19.738 158.786   3176
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.58 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.26), residues: 1007
  helix:  1.26 (0.23), residues: 520
  sheet:  1.43 (0.58), residues: 66
  loop : -0.94 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 938 
 TYR   0.013   0.001   TYR A 973 
 PHE   0.024   0.002   PHE A1181 
 TRP   0.005   0.001   TRP A 464 
 HIS   0.004   0.001   HIS A 930 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.15 (12062)
  covalent geometry    : angle       0.57126 /  0.32 (16948)
  hydrogen bonds       : bond        0.04792 /  3.01 (  515)
  hydrogen bonds       : angle       4.60451 /  3.37 ( 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
  89 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7378 (tmm) cc_final: 0.6992 (tmm)
REVERT: A   60 GLU cc_start: 0.9619 (pm20) cc_final: 0.9336 (pm20)
REVERT: A  102 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8627 (pt0)
REVERT: A  321 MET cc_start: 0.9708 (mmp) cc_final: 0.9485 (mmp)
REVERT: A  524 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9202 (pp)
REVERT: A  629 ARG cc_start: 0.9298 (mtt180) cc_final: 0.8782 (mmt-90)
REVERT: A  631 MET cc_start: 0.9409 (tpt) cc_final: 0.9099 (mmm)
REVERT: A  746 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8900 (mm-30)
REVERT: A  951 ARG cc_start: 0.9538 (mpp-170) cc_final: 0.9239 (mmt90)
REVERT: A 1096 LYS cc_start: 0.9068 (tptt) cc_final: 0.8574 (ttmm)
REVERT: A 1198 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9240 (mm)
  outliers start: 23
  outliers final: 16
  residues processed: 84
  average time/residue: 0.0935
  time to fit residues: 11.6585
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  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  102 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  364 ASP
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  680 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue  748 VAL
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 1337 THR
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:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 90 optimal weight:   20.0000
   chunk 68 optimal weight:    7.9990
   chunk 52 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    4.7990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.040315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.029090 restraints weight = 101345.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.030124 restraints weight = 55235.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.030807 restraints weight = 37470.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.031247 restraints weight = 29099.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.031563 restraints weight = 24623.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.5345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12062  Z= 0.163
  Angle     :  0.564  11.923  16948  Z= 0.315
  Chirality :  0.039   0.262   1959
  Planarity :  0.003   0.053   1601
  Dihedral  : 19.768 159.096   3176
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.13 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.26), residues: 1007
  helix:  1.27 (0.22), residues: 520
  sheet:  1.35 (0.59), residues: 66
  loop : -0.95 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  63 
 TYR   0.011   0.001   TYR A1237 
 PHE   0.014   0.002   PHE A 587 
 TRP   0.005   0.001   TRP A 464 
 HIS   0.005   0.001   HIS A 930 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.16 (12062)
  covalent geometry    : angle       0.56390 /  0.32 (16948)
  hydrogen bonds       : bond        0.04922 /  3.11 (  515)
  hydrogen bonds       : angle       4.60179 /  3.37 ( 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
  84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 60
  time to evaluate  : 0.354 
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: 0.7417 (tmm) cc_final: 0.7026 (tmm)
REVERT: A   60 GLU cc_start: 0.9607 (pm20) cc_final: 0.9316 (pm20)
REVERT: A  102 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8602 (pt0)
REVERT: A  383 MET cc_start: 0.7522 (mtt) cc_final: 0.6976 (ttt)
REVERT: A  524 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9215 (pp)
REVERT: A  629 ARG cc_start: 0.9335 (mtt180) cc_final: 0.8840 (mmt-90)
REVERT: A  631 MET cc_start: 0.9408 (tpt) cc_final: 0.9084 (mmm)
REVERT: A  746 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8958 (mm-30)
REVERT: A  951 ARG cc_start: 0.9539 (mpp-170) cc_final: 0.9214 (mmt90)
REVERT: A 1198 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9224 (mm)
  outliers start: 24
  outliers final: 18
  residues processed: 78
  average time/residue: 0.0863
  time to fit residues: 10.1682
Evaluate side-chains
  79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 57
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  102 GLU
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  513 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  680 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 1260 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 74 optimal weight:   20.0000
   chunk 68 optimal weight:    8.9990
   chunk 102 optimal weight:   40.0000
   chunk 43 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 78 optimal weight:    9.9990
   chunk 103 optimal weight:   30.0000
   chunk 3 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   overall best weight:    8.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 595 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.038456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.027693 restraints weight = 105625.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.028656 restraints weight = 57607.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.029308 restraints weight = 39313.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.029721 restraints weight = 30456.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.030023 restraints weight = 25811.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.6116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.094  12062  Z= 0.254
  Angle     :  0.675  10.890  16948  Z= 0.373
  Chirality :  0.042   0.205   1959
  Planarity :  0.005   0.054   1601
  Dihedral  : 20.009 159.249   3176
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 13.24 %
    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:  0.03 (0.26), residues: 1007
  helix:  0.87 (0.22), residues: 520
  sheet:  1.08 (0.68), residues: 56
  loop : -1.17 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 139 
 TYR   0.021   0.002   TYR A 973 
 PHE   0.022   0.002   PHE A 970 
 TRP   0.012   0.002   TRP A 659 
 HIS   0.009   0.002   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00471 /  0.25 (12062)
  covalent geometry    : angle       0.67486 /  0.37 (16948)
  hydrogen bonds       : bond        0.06438 /  4.23 (  515)
  hydrogen bonds       : angle       4.92958 /  3.60 ( 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: 27
    poor density    : 58
  time to evaluate  : 0.230 
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: 0.7605 (tmm) cc_final: 0.7219 (tmm)
REVERT: A   60 GLU cc_start: 0.9635 (pm20) cc_final: 0.9376 (pm20)
REVERT: A  125 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8198 (mm-30)
REVERT: A  161 MET cc_start: 0.9604 (mmt) cc_final: 0.9289 (mmm)
REVERT: A  321 MET cc_start: 0.9657 (mmp) cc_final: 0.9331 (mmp)
REVERT: A  383 MET cc_start: 0.7541 (mtt) cc_final: 0.7115 (ttt)
REVERT: A  524 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9327 (pp)
REVERT: A  629 ARG cc_start: 0.9354 (mtt180) cc_final: 0.8855 (mmt-90)
REVERT: A  631 MET cc_start: 0.9376 (tpt) cc_final: 0.9061 (mmm)
REVERT: A  746 GLU cc_start: 0.9288 (mp0) cc_final: 0.9020 (mm-30)
REVERT: A  951 ARG cc_start: 0.9544 (mpp-170) cc_final: 0.9186 (mmt90)
REVERT: A 1198 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9181 (mm)
  outliers start: 27
  outliers final: 20
  residues processed: 79
  average time/residue: 0.1036
  time to fit residues: 11.9747
Evaluate side-chains
  76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 53
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 VAL
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  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  680 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  744 VAL
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 1260 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 86 optimal weight:    8.9990
   chunk 83 optimal weight:    2.9990
   chunk 64 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   chunk 4 optimal weight:   20.0000
   chunk 55 optimal weight:    8.9990
   chunk 111 optimal weight:   40.0000
   chunk 78 optimal weight:   20.0000
   chunk 36 optimal weight:    9.9990
   chunk 46 optimal weight:   20.0000
   overall best weight:    6.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 723 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.038503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.027643 restraints weight = 104012.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.028605 restraints weight = 57222.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.029271 restraints weight = 39148.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.029693 restraints weight = 30431.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.029964 restraints weight = 25830.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.6338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12062  Z= 0.203
  Angle     :  0.624  11.506  16948  Z= 0.343
  Chirality :  0.040   0.210   1959
  Planarity :  0.004   0.055   1601
  Dihedral  : 20.032 158.386   3176
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 14.66 %
    Favored  : 83.15 %
  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:  0.09 (0.26), residues: 1007
  helix:  0.86 (0.22), residues: 521
  sheet:  0.98 (0.66), residues: 56
  loop : -1.05 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 139 
 TYR   0.020   0.002   TYR A1356 
 PHE   0.036   0.002   PHE A1204 
 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        0.00373 /  0.20 (12062)
  covalent geometry    : angle       0.62380 /  0.34 (16948)
  hydrogen bonds       : bond        0.05283 /  3.35 (  515)
  hydrogen bonds       : angle       4.80500 /  3.52 ( 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
  74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7669 (tmm) cc_final: 0.7284 (tmm)
REVERT: A   60 GLU cc_start: 0.9625 (pm20) cc_final: 0.9344 (pm20)
REVERT: A  125 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8126 (mm-30)
REVERT: A  161 MET cc_start: 0.9498 (mmt) cc_final: 0.9201 (mmm)
REVERT: A  321 MET cc_start: 0.9631 (mmp) cc_final: 0.9298 (mmp)
REVERT: A  383 MET cc_start: 0.7610 (mtt) cc_final: 0.7241 (ttt)
REVERT: A  524 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9306 (pp)
REVERT: A  629 ARG cc_start: 0.9348 (mtt180) cc_final: 0.8820 (mmt-90)
REVERT: A  631 MET cc_start: 0.9374 (tpt) cc_final: 0.9081 (mmm)
REVERT: A  746 GLU cc_start: 0.9236 (mp0) cc_final: 0.8914 (mm-30)
REVERT: A  951 ARG cc_start: 0.9555 (mpp-170) cc_final: 0.9220 (mmt90)
REVERT: A 1089 MET cc_start: 0.8754 (mmt) cc_final: 0.8494 (tpt)
REVERT: A 1198 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9181 (mm)
  outliers start: 20
  outliers final: 16
  residues processed: 71
  average time/residue: 0.0877
  time to fit residues: 9.3573
Evaluate side-chains
  71 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 52
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 VAL
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  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  680 LEU
Chi-restraints excluded: chain A residue  693 PHE
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 1260 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 95 optimal weight:    1.9990
   chunk 3 optimal weight:   20.0000
   chunk 37 optimal weight:    8.9990
   chunk 86 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 71 optimal weight:   20.0000
   chunk 38 optimal weight:    8.9990
   overall best weight:    5.5990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.038459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.027603 restraints weight = 105098.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.028561 restraints weight = 58097.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.029177 restraints weight = 39693.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.029630 restraints weight = 31090.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.029891 restraints weight = 26357.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.6492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12062  Z= 0.181
  Angle     :  0.607  11.264  16948  Z= 0.335
  Chirality :  0.040   0.207   1959
  Planarity :  0.004   0.054   1601
  Dihedral  : 19.999 158.849   3176
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.77 %
    Favored  : 82.93 %
  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:  0.24 (0.26), residues: 1007
  helix:  1.00 (0.22), residues: 521
  sheet:  1.10 (0.66), residues: 57
  loop : -1.01 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 139 
 TYR   0.039   0.002   TYR A 943 
 PHE   0.015   0.002   PHE A 970 
 TRP   0.007   0.001   TRP A 464 
 HIS   0.005   0.001   HIS A 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.18 (12062)
  covalent geometry    : angle       0.60730 /  0.33 (16948)
  hydrogen bonds       : bond        0.05211 /  3.31 (  515)
  hydrogen bonds       : angle       4.73192 /  3.47 ( 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
  74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 53
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7690 (tmm) cc_final: 0.7309 (tmm)
REVERT: A   60 GLU cc_start: 0.9629 (pm20) cc_final: 0.9354 (pm20)
REVERT: A  125 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8089 (mm-30)
REVERT: A  161 MET cc_start: 0.9526 (mmt) cc_final: 0.9230 (mmm)
REVERT: A  321 MET cc_start: 0.9626 (mmp) cc_final: 0.9294 (mmp)
REVERT: A  383 MET cc_start: 0.7560 (mtt) cc_final: 0.7194 (ttt)
REVERT: A  495 MET cc_start: 0.9208 (pmm) cc_final: 0.8813 (pmm)
REVERT: A  524 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9276 (pp)
REVERT: A  564 LEU cc_start: 0.9752 (tp) cc_final: 0.9503 (mt)
REVERT: A  629 ARG cc_start: 0.9352 (mtt180) cc_final: 0.8832 (mmt-90)
REVERT: A  631 MET cc_start: 0.9386 (tpt) cc_final: 0.9078 (mmm)
REVERT: A  746 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8913 (mm-30)
REVERT: A  951 ARG cc_start: 0.9510 (mpp-170) cc_final: 0.9309 (mtm-85)
REVERT: A 1089 MET cc_start: 0.8781 (mmt) cc_final: 0.8268 (tpp)
REVERT: A 1198 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9184 (mm)
  outliers start: 21
  outliers final: 17
  residues processed: 71
  average time/residue: 0.0802
  time to fit residues: 8.7685
Evaluate side-chains
  73 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 52
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 VAL
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  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  680 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 1260 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 86 optimal weight:    9.9990
   chunk 79 optimal weight:    9.9990
   chunk 50 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0770
   chunk 16 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 7 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 43 optimal weight:   20.0000
   chunk 20 optimal weight:   10.0000
   overall best weight:    2.1542

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.039554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.028461 restraints weight = 102235.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.029472 restraints weight = 56133.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.030158 restraints weight = 38122.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.030568 restraints weight = 29509.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.030889 restraints weight = 25113.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.6488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12062  Z= 0.116
  Angle     :  0.577  11.520  16948  Z= 0.311
  Chirality :  0.039   0.206   1959
  Planarity :  0.003   0.051   1601
  Dihedral  : 19.848 159.176   3176
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 15.75 %
    Favored  : 82.82 %
  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:  0.59 (0.27), residues: 1007
  helix:  1.26 (0.23), residues: 521
  sheet:  1.13 (0.62), residues: 67
  loop : -0.82 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 691 
 TYR   0.015   0.001   TYR A 943 
 PHE   0.036   0.001   PHE A1204 
 TRP   0.004   0.001   TRP A 464 
 HIS   0.004   0.001   HIS A 930 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00212 /  0.12 (12062)
  covalent geometry    : angle       0.57715 /  0.31 (16948)
  hydrogen bonds       : bond        0.04381 /  2.67 (  515)
  hydrogen bonds       : angle       4.48232 /  3.29 ( 1368)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1626.56 seconds
wall clock time: 28 minutes 55.86 seconds (1735.86 seconds total)