Starting phenix.real_space_refine
on Sat Aug 23 15:44:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iyq_35827/08_2025/8iyq_35827_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iyq_35827/08_2025/8iyq_35827.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iyq_35827/08_2025/8iyq_35827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iyq_35827/08_2025/8iyq_35827.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iyq_35827/08_2025/8iyq_35827_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iyq_35827/08_2025/8iyq_35827_neut.cif"
  }
  resolution = 2.46
  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=   0.001 sd=   0.018
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     147      5.49       5
     S      19      5.16       5
     C    7786      2.51       5
     N    2284      2.21       5
     O    2845      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13081
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9980
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1198, 9972
          Classifications: {'peptide': 1198}
          Link IDs: {'PTRANS': 30, 'TRANS': 1167}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 1198, 9972
          Classifications: {'peptide': 1198}
          Link IDs: {'PTRANS': 30, 'TRANS': 1167}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 10172
    Chain: "F"
      Number of atoms: 561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 561
          Classifications: {'DNA': 28}
          Link IDs: {'rna3p': 27}
    Chain: "O"
      Number of atoms: 2332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 2332
          Classifications: {'RNA': 109}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 59, 'rna3p_pyr': 43}
          Link IDs: {'rna2p': 6, 'rna3p': 102}
          Chain breaks: 1
    Chain: "S"
      Number of atoms: 208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 208
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AASP A 672 " occ=0.44
      ... (14 atoms not shown)
      pdb=" OD2BASP A 672 " occ=0.56
  Time building chain proxies: 5.10, per 1000 atoms: 0.39
  Number of scatterers: 13081
  At special positions: 0
  Unit cell: (100.672, 112.58, 150.468, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P     147     15.00
     O    2845      8.00
     N    2284      7.00
     C    7786      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.17
  Conformation dependent library (CDL) restraints added in 940.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2282

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 16 sheets defined
      45.2% alpha, 12.1% beta
      62 base pairs and 77 stacking pairs defined.
    Time for finding SS restraints: 2.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 50
      removed outlier: 4.246A  pdb=" N   GLY A  50 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 89
    Processing helix  chain 'A' and resid 92 through 97
    Processing helix  chain 'A' and resid 129 through 144
    Processing helix  chain 'A' and resid 150 through 152
      No H-bonds generated for 'chain 'A' and resid 150 through 152'
    Processing helix  chain 'A' and resid 153 through 163
      removed outlier: 3.707A  pdb=" N   HIS A 157 " --> pdb=" O   TRP A 153 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ILE A 163 " --> pdb=" O   ARG A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 182
    Processing helix  chain 'A' and resid 273 through 288
    Processing helix  chain 'A' and resid 291 through 303
    Processing helix  chain 'A' and resid 317 through 334
      removed outlier: 4.247A  pdb=" N   TYR A 321 " --> pdb=" O   GLU A 317 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLU A 334 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 340
      removed outlier: 6.249A  pdb=" N   GLU A 338 " --> pdb=" O   PHE A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 353
    Processing helix  chain 'A' and resid 356 through 364
    Processing helix  chain 'A' and resid 367 through 374
    Processing helix  chain 'A' and resid 386 through 390
    Processing helix  chain 'A' and resid 419 through 434
    Processing helix  chain 'A' and resid 452 through 465
      removed outlier: 3.526A  pdb=" N   THR A 465 " --> pdb=" O   GLU A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 478
      removed outlier: 3.677A  pdb=" N   PHE A 478 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 510
      removed outlier: 3.592A  pdb=" N   THR A 502 " --> pdb=" O   ASN A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 534
    Processing helix  chain 'A' and resid 536 through 551
    Processing helix  chain 'A' and resid 556 through 563
    Processing helix  chain 'A' and resid 576 through 588
      Proline residue:  A 585  - end of helix
    Processing helix  chain 'A' and resid 589 through 593
    Processing helix  chain 'A' and resid 594 through 598
    Processing helix  chain 'A' and resid 599 through 612
    Processing helix  chain 'A' and resid 619 through 626
      removed outlier: 3.585A  pdb=" N   ARG A 623 " --> pdb=" O   LYS A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 629
      No H-bonds generated for 'chain 'A' and resid 627 through 629'
    Processing helix  chain 'A' and resid 631 through 635
    Processing helix  chain 'A' and resid 639 through 649
    Processing helix  chain 'A' and resid 662 through 672
      removed outlier: 3.990A  pdb=" N   LEU A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 703
    Processing helix  chain 'A' and resid 932 through 943
      removed outlier: 4.251A  pdb=" N   LYS A 936 " --> pdb=" O   ARG A 932 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   TYR A 937 " --> pdb=" O   TYR A 933 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ILE A 938 " --> pdb=" O   ILE A 934 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER A 939 " --> pdb=" O   SER A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 976
    Processing helix  chain 'A' and resid 977 through 998
      Proline residue:  A 988  - end of helix
    Processing helix  chain 'A' and resid 1017 through 1021
    Processing helix  chain 'A' and resid 1032 through 1044
    Processing helix  chain 'A' and resid 1045 through 1054
    Processing helix  chain 'A' and resid 1059 through 1070
      removed outlier: 3.900A  pdb=" N   ARG A1063 " --> pdb=" O   SER A1059 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ASP A1065 " --> pdb=" O   THR A1061 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   LEU A1066 " --> pdb=" O   LYS A1062 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1111
    Processing helix  chain 'A' and resid 1193 through 1198
    Processing helix  chain 'A' and resid 1202 through 1216
    Processing helix  chain 'A' and resid 1219 through 1224
    Processing helix  chain 'A' and resid 1225 through 1235
    Processing helix  chain 'A' and resid 1236 through 1240
    Processing helix  chain 'A' and resid 1265 through 1270
      removed outlier: 3.818A  pdb=" N   LYS A1269 " --> pdb=" O   GLY A1266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1299 through 1309
    Processing helix  chain 'A' and resid 1353 through 1358
    Processing helix  chain 'A' and resid 1410 through 1415
      removed outlier: 4.159A  pdb=" N   THR A1414 " --> pdb=" O   ARG A1410 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 715
      removed outlier: 6.534A  pdb=" N   LYS A  21 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   ILE A  31 " --> pdb=" O   LYS A  21 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ASP A  23 " --> pdb=" O   GLY A  29 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   GLY A  29 " --> pdb=" O   ASP A  23 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100
      removed outlier: 3.754A  pdb=" N   LYS A 107 " --> pdb=" O   ASP A 100 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 121
    Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 205
    Processing sheet with id=AA5, first strand: chain 'A' and resid 211 through 215
      removed outlier: 4.339A  pdb=" N   GLU A 214 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 400
      removed outlier: 5.338A  pdb=" N   LEU A 412 " --> pdb=" O   CYS A 393 " (cutoff:3.500A)
      removed outlier: 9.568A  pdb=" N   LEU A 395 " --> pdb=" O   GLN A 410 " (cutoff:3.500A)
      removed outlier: 10.678A  pdb=" N   GLN A 410 " --> pdb=" O   LEU A 395 " (cutoff:3.500A)
      removed outlier: 10.045A  pdb=" N   PHE A 397 " --> pdb=" O   HIS A 408 " (cutoff:3.500A)
      removed outlier: 11.277A  pdb=" N   HIS A 408 " --> pdb=" O   PHE A 397 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 437 through 438
    Processing sheet with id=AA8, first strand: chain 'A' and resid 468 through 469
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1003 through 1006
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1071 through 1072
      removed outlier: 4.016A  pdb=" N   GLN A1094 " --> pdb=" O   LYS A1072 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1124 through 1126
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1130 through 1137
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1166 through 1168
      removed outlier: 4.349A  pdb=" N   LEU A1181 " --> pdb=" O   VAL A1168 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1260 through 1261
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1293 through 1297
      removed outlier: 6.065A  pdb=" N   PHE A1283 " --> pdb=" O   ASP A1327 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ASP A1327 " --> pdb=" O   PHE A1283 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   VAL A1285 " --> pdb=" O   LEU A1325 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1370 through 1375
      removed outlier: 6.924A  pdb=" N   GLU A1370 " --> pdb=" O   THR A1366 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   THR A1366 " --> pdb=" O   GLU A1370 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   TYR A1372 " --> pdb=" O   GLU A1364 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   LEU A1333 " --> pdb=" O   ILE A1418 " (cutoff:3.500A)

    412 hydrogen bonds defined for protein.
    1146 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      152 hydrogen bonds
      292 hydrogen bond angles
      0 basepair planarities
      62 basepair parallelities
      77 stacking parallelities
  Total time for adding SS restraints: 3.84

  Time building geometry restraints manager: 1.54 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1898
        1.31 -     1.44: 4460
        1.44 -     1.56: 6978
        1.56 -     1.68: 291
        1.68 -     1.81: 31
  Bond restraints: 13658
  Sorted by residual:
  bond pdb=" C   VAL A 622 "
       pdb=" O   VAL A 622 "
    ideal  model  delta    sigma   weight residual
    1.236  1.188  0.048 1.11e-02 8.12e+03 1.89e+01
  bond pdb=" CA  THR A 502 "
       pdb=" C   THR A 502 "
    ideal  model  delta    sigma   weight residual
    1.524  1.487  0.038 1.24e-02 6.50e+03 9.17e+00
  bond pdb=" N   LYS A1058 "
       pdb=" CA  LYS A1058 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.034 1.29e-02 6.01e+03 6.99e+00
  bond pdb=" CA  VAL A 622 "
       pdb=" C   VAL A 622 "
    ideal  model  delta    sigma   weight residual
    1.524  1.494  0.030 1.18e-02 7.18e+03 6.57e+00
  bond pdb=" C   THR A 502 "
       pdb=" O   THR A 502 "
    ideal  model  delta    sigma   weight residual
    1.236  1.208  0.028 1.15e-02 7.56e+03 5.95e+00
  ... (remaining 13653 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 18795
        1.75 -     3.50: 254
        3.50 -     5.24: 29
        5.24 -     6.99: 7
        6.99 -     8.74: 1
  Bond angle restraints: 19086
  Sorted by residual:
  angle pdb=" C4'   G O  89 "
        pdb=" C3'   G O  89 "
        pdb=" O3'   G O  89 "
      ideal   model   delta    sigma   weight residual
     113.00  104.26    8.74 1.50e+00 4.44e-01 3.40e+01
  angle pdb=" C   VAL A 622 "
        pdb=" CA  VAL A 622 "
        pdb=" CB  VAL A 622 "
      ideal   model   delta    sigma   weight residual
     111.81  105.81    6.00 1.25e+00 6.40e-01 2.31e+01
  angle pdb=" N   ILE A1343 "
        pdb=" CA  ILE A1343 "
        pdb=" C   ILE A1343 "
      ideal   model   delta    sigma   weight residual
     106.55  112.86   -6.31 1.45e+00 4.76e-01 1.89e+01
  angle pdb=" O3'   G O  89 "
        pdb=" C3'   G O  89 "
        pdb=" C2'   G O  89 "
      ideal   model   delta    sigma   weight residual
     113.70  120.22   -6.52 1.50e+00 4.44e-01 1.89e+01
  angle pdb=" N   ASP A 211 "
        pdb=" CA  ASP A 211 "
        pdb=" C   ASP A 211 "
      ideal   model   delta    sigma   weight residual
     110.30  104.32    5.98 1.50e+00 4.44e-01 1.59e+01
  ... (remaining 19081 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.78: 7427
       23.78 -    47.55: 563
       47.55 -    71.33: 221
       71.33 -    95.11: 36
       95.11 -   118.88: 2
  Dihedral angle restraints: 8249
    sinusoidal: 4722
      harmonic: 3527
  Sorted by residual:
  dihedral pdb=" C4'   G O 107 "
           pdb=" C3'   G O 107 "
           pdb=" O3'   G O 107 "
           pdb=" P     C O 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00  101.62  118.38     1      3.50e+01 8.16e-04 1.16e+01
  dihedral pdb=" CA  ASP A 517 "
           pdb=" CB  ASP A 517 "
           pdb=" CG  ASP A 517 "
           pdb=" OD1 ASP A 517 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.89   56.89     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CB  GLU A1255 "
           pdb=" CG  GLU A1255 "
           pdb=" CD  GLU A1255 "
           pdb=" OE1 GLU A1255 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.77  -86.77     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 8246 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1709
       0.040 -    0.079: 323
       0.079 -    0.119: 109
       0.119 -    0.159: 15
       0.159 -    0.198: 2
  Chirality restraints: 2158
  Sorted by residual:
  chirality pdb=" C2'   G O  89 "
            pdb=" C3'   G O  89 "
            pdb=" O2'   G O  89 "
            pdb=" C1'   G O  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.55   -0.20 2.00e-01 2.50e+01 9.84e-01
  chirality pdb=" C1'   C O  36 "
            pdb=" O4'   C O  36 "
            pdb=" C2'   C O  36 "
            pdb=" N1    C O  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.31    0.16 2.00e-01 2.50e+01 6.30e-01
  chirality pdb=" C2'   G O 106 "
            pdb=" C3'   G O 106 "
            pdb=" O2'   G O 106 "
            pdb=" C1'   G O 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.60   -0.16 2.00e-01 2.50e+01 6.06e-01
  ... (remaining 2155 not shown)

  Planarity restraints: 1901
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 645 "   -0.025 2.00e-02 2.50e+03   1.77e-02 6.26e+00
        pdb=" CG  TYR A 645 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 645 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 645 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 645 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 645 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 645 "   -0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR A 645 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 479 "    0.009 2.00e-02 2.50e+03   1.84e-02 3.40e+00
        pdb=" C   LYS A 479 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   LYS A 479 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A 480 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C O  36 "   -0.020 2.00e-02 2.50e+03   1.17e-02 3.06e+00
        pdb=" N1    C O  36 "    0.027 2.00e-02 2.50e+03
        pdb=" C2    C O  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2    C O  36 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    C O  36 "    0.000 2.00e-02 2.50e+03
        pdb=" C4    C O  36 "   -0.006 2.00e-02 2.50e+03
        pdb=" N4    C O  36 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    C O  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    C O  36 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1898 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3867
        2.82 -     3.34: 12264
        3.34 -     3.86: 23581
        3.86 -     4.38: 28162
        4.38 -     4.90: 43444
  Nonbonded interactions: 111318
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A1163 "
            pdb=" OP2  DC F  36 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O2'   G O 107 "
            pdb=" OP1   C O 108 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   PRO A1244 "
            pdb=" O2'   U O  30 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   VAL A 243 "
            pdb=" OD1 ASP A 244 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OD1 ASN A1129 "
            pdb=" O2'   C O  87 "
     model   vdw
     2.331 3.040
  ... (remaining 111313 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.44 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     18.920
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
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   0.048  13658  Z= 0.179
  Angle     :  0.520   8.741  19086  Z= 0.312
  Chirality :  0.037   0.198   2158
  Planarity :  0.003   0.043   1901
  Dihedral  : 18.287 118.883   5967
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  1.09 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.25), residues: 1195
  helix:  1.79 (0.25), residues: 465
  sheet: -0.90 (0.43), residues: 130
  loop : -0.69 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1145 
 TYR   0.041   0.001   TYR A 645 
 PHE   0.017   0.001   PHE A 425 
 TRP   0.010   0.001   TRP A 487 
 HIS   0.004   0.001   HIS A 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (13658)
  covalent geometry    : angle       0.52025 (19086)
  hydrogen bonds       : bond        0.13160 (  564)
  hydrogen bonds       : angle       5.30537 ( 1438)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 233
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 THR cc_start: 0.8309 (m) cc_final: 0.7710 (t)
REVERT: A   41 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6381 (ttp)
REVERT: A   63 LYS cc_start: 0.7480 (ttpp) cc_final: 0.7150 (ttpp)
REVERT: A  102 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7367 (mt-10)
REVERT: A  138 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6482 (mp0)
REVERT: A  181 HIS cc_start: 0.7531 (m90) cc_final: 0.6995 (m-70)
REVERT: A  188 LEU cc_start: 0.7854 (tp) cc_final: 0.7616 (tp)
REVERT: A  272 LYS cc_start: 0.7280 (ttmm) cc_final: 0.7019 (ttmm)
REVERT: A  290 LYS cc_start: 0.7760 (mtmm) cc_final: 0.7525 (mtmm)
REVERT: A  349 ILE cc_start: 0.7139 (mt) cc_final: 0.6938 (mp)
REVERT: A  374 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7603 (mm-30)
REVERT: A  432 PHE cc_start: 0.7300 (m-10) cc_final: 0.7087 (m-10)
REVERT: A  433 ASN cc_start: 0.7151 (m-40) cc_final: 0.6926 (m-40)
REVERT: A  449 PHE cc_start: 0.8000 (m-10) cc_final: 0.7670 (m-10)
REVERT: A  461 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6666 (tp30)
REVERT: A  468 GLU cc_start: 0.7469 (tt0) cc_final: 0.7264 (tt0)
REVERT: A  472 LYS cc_start: 0.7349 (tppt) cc_final: 0.7105 (tppt)
REVERT: A  491 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7641 (mt-10)
REVERT: A  518 PHE cc_start: 0.7996 (t80) cc_final: 0.7697 (t80)
REVERT: A  535 ASN cc_start: 0.7745 (p0) cc_final: 0.7454 (p0)
REVERT: A  554 ASP cc_start: 0.7574 (t0) cc_final: 0.7255 (p0)
REVERT: A  559 PHE cc_start: 0.7501 (t80) cc_final: 0.7248 (t80)
REVERT: A  571 GLU cc_start: 0.7853 (pt0) cc_final: 0.7601 (pt0)
REVERT: A  608 LYS cc_start: 0.5916 (mttp) cc_final: 0.5555 (tmtt)
REVERT: A  706 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7903 (tttt)
REVERT: A  707 ASP cc_start: 0.7878 (t70) cc_final: 0.7611 (t0)
REVERT: A  954 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6872 (mm-30)
REVERT: A  971 GLN cc_start: 0.6914 (tp-100) cc_final: 0.6517 (tp40)
REVERT: A 1107 LYS cc_start: 0.7213 (tttp) cc_final: 0.7004 (ttmt)
REVERT: A 1132 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7344 (mm-30)
REVERT: A 1144 GLU cc_start: 0.7746 (pt0) cc_final: 0.7529 (pt0)
REVERT: A 1145 ARG cc_start: 0.7460 (mtp85) cc_final: 0.7206 (mtp85)
REVERT: A 1159 MET cc_start: 0.8665 (mtm) cc_final: 0.8404 (mtp)
REVERT: A 1177 LYS cc_start: 0.8241 (tmtt) cc_final: 0.7940 (tmtt)
REVERT: A 1221 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7323 (mm-30)
REVERT: A 1227 GLU cc_start: 0.7263 (mp0) cc_final: 0.6964 (mp0)
REVERT: A 1237 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7264 (tp30)
REVERT: A 1269 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7818 (mtmp)
REVERT: A 1290 LYS cc_start: 0.7071 (mmpt) cc_final: 0.6832 (mmpt)
REVERT: A 1319 GLU cc_start: 0.7068 (mp0) cc_final: 0.6639 (mp0)
REVERT: A 1388 LYS cc_start: 0.7224 (mtpp) cc_final: 0.7001 (mtpp)
REVERT: A 1425 ASN cc_start: 0.7406 (m110) cc_final: 0.6933 (m-40)
  outliers start: 6
  outliers final: 2
  residues processed: 237
  average time/residue: 0.8614
  time to fit residues: 217.2968
Evaluate side-chains
  210 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 207
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue  488 ASN
Chi-restraints excluded: chain A residue  932 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0470
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.7080

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

Flipped N/Q/H residues before XYZ refinement:
A  57 GLN
A 283 GLN
A 454 GLN
A 458 ASN
A 594 ASN
** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1033 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.140587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.113572 restraints weight = 36014.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.38
r_work: 0.3340 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3341
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13658  Z= 0.180
  Angle     :  0.544   6.985  19086  Z= 0.301
  Chirality :  0.040   0.214   2158
  Planarity :  0.004   0.044   1901
  Dihedral  : 18.796 115.313   3380
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  9.62 %
    Favored  : 89.20 %
  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 aren not related in a simple way.
  whole:  0.29 (0.25), residues: 1195
  helix:  1.49 (0.24), residues: 475
  sheet: -0.88 (0.42), residues: 140
  loop : -0.58 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1410 
 TYR   0.041   0.002   TYR A 645 
 PHE   0.024   0.002   PHE A 425 
 TRP   0.026   0.002   TRP A 487 
 HIS   0.005   0.001   HIS A1048 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (13658)
  covalent geometry    : angle       0.54374 (19086)
  hydrogen bonds       : bond        0.04801 (  564)
  hydrogen bonds       : angle       3.89876 ( 1438)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 222
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 THR cc_start: 0.8773 (m) cc_final: 0.8551 (t)
REVERT: A   41 MET cc_start: 0.7268 (ttp) cc_final: 0.6870 (ttp)
REVERT: A  181 HIS cc_start: 0.7842 (m90) cc_final: 0.7577 (m-70)
REVERT: A  374 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7716 (mp0)
REVERT: A  486 ARG cc_start: 0.7839 (ptm-80) cc_final: 0.7525 (ptm-80)
REVERT: A  518 PHE cc_start: 0.8378 (t80) cc_final: 0.8166 (t80)
REVERT: A  550 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7992 (mtmm)
REVERT: A  707 ASP cc_start: 0.7854 (t70) cc_final: 0.7576 (t0)
REVERT: A  938 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8289 (tt)
REVERT: A  941 ILE cc_start: 0.8609 (mm) cc_final: 0.8364 (tp)
REVERT: A  970 THR cc_start: 0.7949 (t) cc_final: 0.7628 (m)
REVERT: A 1005 TRP cc_start: 0.8404 (t-100) cc_final: 0.8085 (t-100)
REVERT: A 1159 MET cc_start: 0.8726 (mtm) cc_final: 0.8503 (mtp)
REVERT: A 1425 ASN cc_start: 0.8275 (m110) cc_final: 0.7975 (m-40)
  outliers start: 13
  outliers final: 10
  residues processed: 229
  average time/residue: 0.8219
  time to fit residues: 200.7176
Evaluate side-chains
  220 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 209
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  488 ASN
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  932 ARG
Chi-restraints excluded: chain A residue  938 ILE
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1174 LYS
Chi-restraints excluded: chain A residue 1339 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 73 optimal weight:    0.3980
   chunk 114 optimal weight:    0.9980
   chunk 112 optimal weight:    0.9980
   chunk 127 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 283 GLN
A 458 ASN
** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 998 ASN
A1009 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.139728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.112544 restraints weight = 39146.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 2.47
r_work: 0.3323 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3324
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3324
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  13658  Z= 0.211
  Angle     :  0.566   6.607  19086  Z= 0.313
  Chirality :  0.041   0.221   2158
  Planarity :  0.004   0.046   1901
  Dihedral  : 18.757 115.855   3377
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.89 %
    Favored  : 85.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.24), residues: 1195
  helix:  1.22 (0.24), residues: 478
  sheet: -0.51 (0.44), residues: 130
  loop : -0.72 (0.26), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1410 
 TYR   0.034   0.002   TYR A 645 
 PHE   0.023   0.002   PHE A 425 
 TRP   0.024   0.002   TRP A 487 
 HIS   0.007   0.001   HIS A 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (13658)
  covalent geometry    : angle       0.56605 (19086)
  hydrogen bonds       : bond        0.04961 (  564)
  hydrogen bonds       : angle       3.91115 ( 1438)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 221
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 THR cc_start: 0.8747 (m) cc_final: 0.8537 (t)
REVERT: A   41 MET cc_start: 0.7413 (ttp) cc_final: 0.7037 (ttp)
REVERT: A  181 HIS cc_start: 0.8019 (m90) cc_final: 0.7776 (m-70)
REVERT: A  272 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7743 (ttmm)
REVERT: A  374 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7752 (mp0)
REVERT: A  550 LYS cc_start: 0.8271 (mmmm) cc_final: 0.8002 (mtmm)
REVERT: A  569 LYS cc_start: 0.8273 (tttm) cc_final: 0.8072 (tttm)
REVERT: A  707 ASP cc_start: 0.7845 (t70) cc_final: 0.7554 (t0)
REVERT: A  970 THR cc_start: 0.8010 (t) cc_final: 0.7731 (m)
REVERT: A  975 ASP cc_start: 0.7483 (m-30) cc_final: 0.7282 (m-30)
REVERT: A 1005 TRP cc_start: 0.8482 (t-100) cc_final: 0.8174 (t-100)
REVERT: A 1425 ASN cc_start: 0.8345 (m110) cc_final: 0.7994 (m-40)
  outliers start: 18
  outliers final: 11
  residues processed: 226
  average time/residue: 0.7940
  time to fit residues: 191.7961
Evaluate side-chains
  225 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 214
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  337 GLN
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  488 ASN
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  674 LYS
Chi-restraints excluded: chain A residue  932 ARG
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1366 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 42 optimal weight:    0.4980
   chunk 92 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0070
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 283 GLN
A 458 ASN
A 485 HIS
A 594 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.140320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.113063 restraints weight = 41586.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.54
r_work: 0.3328 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  13658  Z= 0.176
  Angle     :  0.540   6.680  19086  Z= 0.298
  Chirality :  0.039   0.224   2158
  Planarity :  0.004   0.045   1901
  Dihedral  : 18.711 117.846   3377
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.34 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.24), residues: 1195
  helix:  1.19 (0.23), residues: 479
  sheet: -0.49 (0.44), residues: 130
  loop : -0.71 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 605 
 TYR   0.031   0.001   TYR A 645 
 PHE   0.023   0.002   PHE A 425 
 TRP   0.022   0.002   TRP A 487 
 HIS   0.009   0.001   HIS A 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (13658)
  covalent geometry    : angle       0.54045 (19086)
  hydrogen bonds       : bond        0.04536 (  564)
  hydrogen bonds       : angle       3.84403 ( 1438)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 221
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 THR cc_start: 0.8754 (m) cc_final: 0.8535 (t)
REVERT: A   41 MET cc_start: 0.7414 (ttp) cc_final: 0.7035 (ttp)
REVERT: A  181 HIS cc_start: 0.7992 (m90) cc_final: 0.7749 (m-70)
REVERT: A  272 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7703 (ttmm)
REVERT: A  374 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7762 (mp0)
REVERT: A  550 LYS cc_start: 0.8261 (mmmm) cc_final: 0.8025 (mtmm)
REVERT: A  569 LYS cc_start: 0.8269 (tttm) cc_final: 0.8033 (tttm)
REVERT: A  597 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7163 (mp0)
REVERT: A  707 ASP cc_start: 0.7886 (t70) cc_final: 0.7595 (t0)
REVERT: A  970 THR cc_start: 0.7984 (t) cc_final: 0.7722 (m)
REVERT: A  998 ASN cc_start: 0.8184 (t0) cc_final: 0.7846 (t0)
REVERT: A 1005 TRP cc_start: 0.8490 (t-100) cc_final: 0.8204 (t-100)
REVERT: A 1290 LYS cc_start: 0.8124 (mmpt) cc_final: 0.7899 (mmpt)
REVERT: A 1425 ASN cc_start: 0.8362 (m110) cc_final: 0.8011 (m-40)
  outliers start: 24
  outliers final: 15
  residues processed: 229
  average time/residue: 0.7411
  time to fit residues: 181.2400
Evaluate side-chains
  229 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 214
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  337 GLN
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  488 ASN
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  932 ARG
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1195 LYS
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1366 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 101 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 84 optimal weight:   40.0000
   chunk 67 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 128 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 113 optimal weight:    0.3980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 283 GLN
A 458 ASN
** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 971 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.139838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.113048 restraints weight = 37722.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 2.58
r_work: 0.3328 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3325
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3325
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13658  Z= 0.190
  Angle     :  0.549   8.958  19086  Z= 0.301
  Chirality :  0.040   0.223   2158
  Planarity :  0.004   0.045   1901
  Dihedral  : 18.684 117.094   3377
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.79 %
    Favored  : 84.12 %
  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 aren not related in a simple way.
  whole:  0.08 (0.24), residues: 1195
  helix:  1.15 (0.23), residues: 478
  sheet: -0.47 (0.44), residues: 130
  loop : -0.71 (0.26), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1410 
 TYR   0.029   0.002   TYR A 645 
 PHE   0.021   0.001   PHE A 425 
 TRP   0.022   0.002   TRP A 641 
 HIS   0.005   0.001   HIS A 651 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (13658)
  covalent geometry    : angle       0.54880 (19086)
  hydrogen bonds       : bond        0.04667 (  564)
  hydrogen bonds       : angle       3.87473 ( 1438)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 220
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 THR cc_start: 0.8746 (m) cc_final: 0.8526 (t)
REVERT: A   41 MET cc_start: 0.7454 (ttp) cc_final: 0.7071 (ttp)
REVERT: A  181 HIS cc_start: 0.8036 (m90) cc_final: 0.7770 (m-70)
REVERT: A  516 ASP cc_start: 0.7597 (p0) cc_final: 0.7363 (p0)
REVERT: A  550 LYS cc_start: 0.8261 (mmmm) cc_final: 0.8014 (mtmm)
REVERT: A  597 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7245 (mp0)
REVERT: A  707 ASP cc_start: 0.7939 (t70) cc_final: 0.7638 (t0)
REVERT: A  970 THR cc_start: 0.7990 (t) cc_final: 0.7706 (m)
REVERT: A  998 ASN cc_start: 0.8196 (t0) cc_final: 0.7845 (t0)
REVERT: A 1005 TRP cc_start: 0.8487 (t-100) cc_final: 0.8239 (t-100)
REVERT: A 1289 GLU cc_start: 0.7727 (pm20) cc_final: 0.7449 (pm20)
REVERT: A 1290 LYS cc_start: 0.8155 (mmpt) cc_final: 0.7942 (mmpt)
REVERT: A 1425 ASN cc_start: 0.8382 (m110) cc_final: 0.8030 (m-40)
  outliers start: 23
  outliers final: 19
  residues processed: 228
  average time/residue: 0.8208
  time to fit residues: 199.8518
Evaluate side-chains
  235 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 216
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  337 GLN
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  488 ASN
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  932 ARG
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1195 LYS
Chi-restraints excluded: chain A residue 1238 LYS
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1366 THR
Chi-restraints excluded: chain A residue 1419 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 12 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 23 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 283 GLN
** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.140297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.113861 restraints weight = 30115.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.17
r_work: 0.3358 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3219
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  13658  Z= 0.182
  Angle     :  0.544   7.055  19086  Z= 0.300
  Chirality :  0.039   0.224   2158
  Planarity :  0.004   0.044   1901
  Dihedral  : 18.654 117.790   3377
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.70 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.24), residues: 1195
  helix:  1.06 (0.23), residues: 478
  sheet: -0.38 (0.45), residues: 128
  loop : -0.73 (0.25), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1410 
 TYR   0.029   0.001   TYR A 645 
 PHE   0.024   0.002   PHE A 518 
 TRP   0.027   0.002   TRP A 641 
 HIS   0.008   0.001   HIS A 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (13658)
  covalent geometry    : angle       0.54393 (19086)
  hydrogen bonds       : bond        0.04576 (  564)
  hydrogen bonds       : angle       3.88679 ( 1438)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 219
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A   12 THR cc_start: 0.8795 (m) cc_final: 0.8560 (t)
REVERT: A   41 MET cc_start: 0.7625 (ttp) cc_final: 0.7233 (ttp)
REVERT: A  181 HIS cc_start: 0.8126 (m90) cc_final: 0.7823 (m-70)
REVERT: A  323 GLU cc_start: 0.7789 (tp30) cc_final: 0.7587 (tp30)
REVERT: A  482 GLU cc_start: 0.7797 (tp30) cc_final: 0.7490 (tp30)
REVERT: A  517 ASP cc_start: 0.6929 (t70) cc_final: 0.6612 (t0)
REVERT: A  550 LYS cc_start: 0.8409 (mmmm) cc_final: 0.8147 (mtmm)
REVERT: A  597 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7558 (mp0)
REVERT: A  970 THR cc_start: 0.8029 (t) cc_final: 0.7746 (m)
REVERT: A  998 ASN cc_start: 0.8300 (t0) cc_final: 0.7941 (t0)
REVERT: A 1005 TRP cc_start: 0.8497 (t-100) cc_final: 0.8273 (t-100)
REVERT: A 1159 MET cc_start: 0.8712 (mtp) cc_final: 0.8478 (mtp)
REVERT: A 1289 GLU cc_start: 0.7997 (pm20) cc_final: 0.7609 (pm20)
REVERT: A 1425 ASN cc_start: 0.8539 (m110) cc_final: 0.8244 (m-40)
  outliers start: 22
  outliers final: 18
  residues processed: 225
  average time/residue: 0.8075
  time to fit residues: 194.2221
Evaluate side-chains
  235 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 217
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  337 GLN
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  488 ASN
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  932 ARG
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1177 LYS
Chi-restraints excluded: chain A residue 1195 LYS
Chi-restraints excluded: chain A residue 1238 LYS
Chi-restraints excluded: chain A residue 1366 THR
Chi-restraints excluded: chain A residue 1419 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 27 optimal weight:    0.4980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 126 optimal weight:    1.9990
   chunk 113 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 283 GLN
A 485 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.139785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.112902 restraints weight = 34586.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.32
r_work: 0.3336 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3336
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3336
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13658  Z= 0.201
  Angle     :  0.561   7.842  19086  Z= 0.308
  Chirality :  0.040   0.223   2158
  Planarity :  0.004   0.045   1901
  Dihedral  : 18.651 117.085   3377
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 15.15 %
    Favored  : 83.12 %
  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 aren not related in a simple way.
  whole: -0.00 (0.24), residues: 1195
  helix:  1.03 (0.23), residues: 478
  sheet: -0.40 (0.45), residues: 129
  loop : -0.74 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1410 
 TYR   0.027   0.002   TYR A 645 
 PHE   0.024   0.002   PHE A 669 
 TRP   0.031   0.002   TRP A 641 
 HIS   0.008   0.001   HIS A 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (13658)
  covalent geometry    : angle       0.56062 (19086)
  hydrogen bonds       : bond        0.04775 (  564)
  hydrogen bonds       : angle       3.89862 ( 1438)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 221
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A   12 THR cc_start: 0.8727 (m) cc_final: 0.8494 (t)
REVERT: A   41 MET cc_start: 0.7455 (ttp) cc_final: 0.7100 (ttp)
REVERT: A  181 HIS cc_start: 0.8056 (m90) cc_final: 0.7798 (m-70)
REVERT: A  323 GLU cc_start: 0.7433 (tp30) cc_final: 0.7187 (tp30)
REVERT: A  516 ASP cc_start: 0.7564 (p0) cc_final: 0.7293 (p0)
REVERT: A  517 ASP cc_start: 0.6586 (t70) cc_final: 0.6300 (t0)
REVERT: A  550 LYS cc_start: 0.8234 (mmmm) cc_final: 0.7985 (mtmm)
REVERT: A  597 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7196 (mp0)
REVERT: A  970 THR cc_start: 0.7970 (t) cc_final: 0.7700 (m)
REVERT: A  998 ASN cc_start: 0.8118 (t0) cc_final: 0.7769 (t0)
REVERT: A 1005 TRP cc_start: 0.8497 (t-100) cc_final: 0.8280 (t-100)
REVERT: A 1159 MET cc_start: 0.8580 (mtp) cc_final: 0.8343 (mtp)
REVERT: A 1425 ASN cc_start: 0.8404 (m110) cc_final: 0.8094 (m-40)
  outliers start: 19
  outliers final: 16
  residues processed: 226
  average time/residue: 0.8309
  time to fit residues: 200.9636
Evaluate side-chains
  233 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 217
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  337 GLN
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  932 ARG
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  995 GLN
Chi-restraints excluded: chain A residue 1195 LYS
Chi-restraints excluded: chain A residue 1238 LYS
Chi-restraints excluded: chain A residue 1366 THR
Chi-restraints excluded: chain A residue 1419 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 122 optimal weight:    1.9990
   chunk 84 optimal weight:   10.0000
   chunk 101 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 112 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0070
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.9402

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

Flipped N/Q/H residues before XYZ refinement:
A 485 HIS
A 488 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.139401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.112188 restraints weight = 38790.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.46
r_work: 0.3320 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3320
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3320
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  13658  Z= 0.221
  Angle     :  0.589   8.891  19086  Z= 0.322
  Chirality :  0.041   0.224   2158
  Planarity :  0.004   0.045   1901
  Dihedral  : 18.642 116.841   3375
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.88 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.24), residues: 1195
  helix:  0.96 (0.23), residues: 478
  sheet: -0.38 (0.45), residues: 129
  loop : -0.75 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1410 
 TYR   0.024   0.002   TYR A 645 
 PHE   0.033   0.002   PHE A 669 
 TRP   0.036   0.002   TRP A 641 
 HIS   0.008   0.001   HIS A 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (13658)
  covalent geometry    : angle       0.58937 (19086)
  hydrogen bonds       : bond        0.04951 (  564)
  hydrogen bonds       : angle       3.93908 ( 1438)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 217
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A   12 THR cc_start: 0.8736 (m) cc_final: 0.8500 (t)
REVERT: A   41 MET cc_start: 0.7472 (ttp) cc_final: 0.7110 (ttp)
REVERT: A  181 HIS cc_start: 0.8082 (m90) cc_final: 0.7834 (m-70)
REVERT: A  323 GLU cc_start: 0.7477 (tp30) cc_final: 0.7207 (tp30)
REVERT: A  482 GLU cc_start: 0.7397 (tp30) cc_final: 0.7145 (tp30)
REVERT: A  516 ASP cc_start: 0.7607 (p0) cc_final: 0.7346 (p0)
REVERT: A  517 ASP cc_start: 0.6671 (t70) cc_final: 0.6398 (t0)
REVERT: A  550 LYS cc_start: 0.8251 (mmmm) cc_final: 0.8003 (mtmm)
REVERT: A  597 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7220 (mp0)
REVERT: A  970 THR cc_start: 0.7990 (t) cc_final: 0.7742 (m)
REVERT: A  998 ASN cc_start: 0.8115 (t0) cc_final: 0.7766 (t0)
REVERT: A 1005 TRP cc_start: 0.8511 (t-100) cc_final: 0.8308 (t-100)
REVERT: A 1159 MET cc_start: 0.8614 (mtp) cc_final: 0.8345 (mtp)
REVERT: A 1425 ASN cc_start: 0.8436 (m110) cc_final: 0.8124 (m-40)
  outliers start: 17
  outliers final: 16
  residues processed: 223
  average time/residue: 0.8266
  time to fit residues: 196.7975
Evaluate side-chains
  232 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 216
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  932 ARG
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  995 GLN
Chi-restraints excluded: chain A residue 1195 LYS
Chi-restraints excluded: chain A residue 1238 LYS
Chi-restraints excluded: chain A residue 1366 THR
Chi-restraints excluded: chain A residue 1419 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 126 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 74 optimal weight:    0.5980
   chunk 100 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 129 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 485 HIS
A 488 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.136424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.108267 restraints weight = 44606.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.72
r_work: 0.3318 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3317
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3317 r_free = 0.3317    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3317 r_free = 0.3317    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3317
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  13658  Z= 0.185
  Angle     :  0.569   8.976  19086  Z= 0.313
  Chirality :  0.040   0.226   2158
  Planarity :  0.004   0.045   1901
  Dihedral  : 18.619 118.602   3375
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.70 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.06 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.00 (0.24), residues: 1195
  helix:  1.04 (0.23), residues: 478
  sheet: -0.39 (0.45), residues: 129
  loop : -0.74 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1410 
 TYR   0.025   0.001   TYR A 645 
 PHE   0.021   0.002   PHE A 425 
 TRP   0.043   0.002   TRP A 641 
 HIS   0.010   0.001   HIS A 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (13658)
  covalent geometry    : angle       0.56941 (19086)
  hydrogen bonds       : bond        0.04585 (  564)
  hydrogen bonds       : angle       3.87457 ( 1438)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 219
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A   12 THR cc_start: 0.8753 (m) cc_final: 0.8508 (t)
REVERT: A   41 MET cc_start: 0.7473 (ttp) cc_final: 0.7094 (ttp)
REVERT: A   60 GLU cc_start: 0.7533 (mp0) cc_final: 0.7199 (mp0)
REVERT: A  181 HIS cc_start: 0.8040 (m90) cc_final: 0.7772 (m-70)
REVERT: A  323 GLU cc_start: 0.7517 (tp30) cc_final: 0.7202 (tp30)
REVERT: A  482 GLU cc_start: 0.7532 (tp30) cc_final: 0.7325 (tp30)
REVERT: A  516 ASP cc_start: 0.7577 (p0) cc_final: 0.7322 (p0)
REVERT: A  517 ASP cc_start: 0.6662 (t70) cc_final: 0.6382 (t0)
REVERT: A  550 LYS cc_start: 0.8258 (mmmm) cc_final: 0.8004 (mtmm)
REVERT: A  597 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7227 (mp0)
REVERT: A  970 THR cc_start: 0.7979 (t) cc_final: 0.7736 (p)
REVERT: A  998 ASN cc_start: 0.8154 (t0) cc_final: 0.7811 (t0)
REVERT: A 1005 TRP cc_start: 0.8502 (t-100) cc_final: 0.8238 (t-100)
REVERT: A 1159 MET cc_start: 0.8603 (mtp) cc_final: 0.8344 (mtp)
REVERT: A 1425 ASN cc_start: 0.8430 (m110) cc_final: 0.8119 (m-40)
  outliers start: 15
  outliers final: 15
  residues processed: 225
  average time/residue: 0.8120
  time to fit residues: 195.1622
Evaluate side-chains
  233 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 218
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  932 ARG
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1195 LYS
Chi-restraints excluded: chain A residue 1238 LYS
Chi-restraints excluded: chain A residue 1366 THR
Chi-restraints excluded: chain A residue 1419 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0570
   chunk 81 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9990
   chunk 110 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
A 485 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.137178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.111370 restraints weight = 23576.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 1.95
r_work: 0.3382 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13658  Z= 0.170
  Angle     :  0.564   8.647  19086  Z= 0.310
  Chirality :  0.039   0.225   2158
  Planarity :  0.004   0.044   1901
  Dihedral  : 18.605 118.888   3375
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.87 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 16.42 %
    Favored  : 82.49 %
  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 aren not related in a simple way.
  whole:  0.01 (0.24), residues: 1195
  helix:  1.06 (0.23), residues: 478
  sheet: -0.41 (0.45), residues: 129
  loop : -0.74 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1410 
 TYR   0.025   0.001   TYR A 645 
 PHE   0.028   0.002   PHE A 669 
 TRP   0.049   0.002   TRP A 641 
 HIS   0.009   0.001   HIS A 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (13658)
  covalent geometry    : angle       0.56404 (19086)
  hydrogen bonds       : bond        0.04440 (  564)
  hydrogen bonds       : angle       3.83962 ( 1438)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 219
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   12 THR cc_start: 0.8779 (m) cc_final: 0.8524 (t)
REVERT: A   41 MET cc_start: 0.7596 (ttp) cc_final: 0.7209 (ttp)
REVERT: A  181 HIS cc_start: 0.8081 (m90) cc_final: 0.7788 (m-70)
REVERT: A  323 GLU cc_start: 0.7746 (tp30) cc_final: 0.7412 (tp30)
REVERT: A  482 GLU cc_start: 0.7660 (tp30) cc_final: 0.7436 (tp30)
REVERT: A  516 ASP cc_start: 0.7716 (p0) cc_final: 0.7452 (p0)
REVERT: A  550 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8113 (mtmm)
REVERT: A  597 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7434 (mp0)
REVERT: A  970 THR cc_start: 0.8019 (t) cc_final: 0.7768 (p)
REVERT: A  998 ASN cc_start: 0.8294 (t0) cc_final: 0.7930 (t0)
REVERT: A 1005 TRP cc_start: 0.8515 (t-100) cc_final: 0.8252 (t-100)
REVERT: A 1159 MET cc_start: 0.8664 (mtp) cc_final: 0.8416 (mtp)
REVERT: A 1425 ASN cc_start: 0.8545 (m110) cc_final: 0.8241 (m-40)
  outliers start: 12
  outliers final: 13
  residues processed: 224
  average time/residue: 0.8449
  time to fit residues: 202.4789
Evaluate side-chains
  229 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 216
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  932 ARG
Chi-restraints excluded: chain A residue 1195 LYS
Chi-restraints excluded: chain A residue 1238 LYS
Chi-restraints excluded: chain A residue 1366 THR
Chi-restraints excluded: chain A residue 1419 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 117 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   chunk 104 optimal weight:    0.0980
   chunk 43 optimal weight:    0.9980
   chunk 112 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 62 optimal weight:    7.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 485 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.140585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.113363 restraints weight = 39682.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.48
r_work: 0.3339 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3338
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3338 r_free = 0.3338    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3338 r_free = 0.3338    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3338
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13658  Z= 0.170
  Angle     :  0.571   9.141  19086  Z= 0.313
  Chirality :  0.039   0.225   2158
  Planarity :  0.004   0.044   1901
  Dihedral  : 18.598 119.024   3375
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.45 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 16.42 %
    Favored  : 82.49 %
  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 aren not related in a simple way.
  whole:  0.02 (0.24), residues: 1195
  helix:  1.06 (0.23), residues: 478
  sheet: -0.41 (0.45), residues: 129
  loop : -0.73 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1410 
 TYR   0.025   0.001   TYR A 645 
 PHE   0.030   0.002   PHE A 669 
 TRP   0.059   0.002   TRP A 641 
 HIS   0.010   0.001   HIS A 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (13658)
  covalent geometry    : angle       0.57109 (19086)
  hydrogen bonds       : bond        0.04414 (  564)
  hydrogen bonds       : angle       3.84398 ( 1438)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6447.39 seconds
wall clock time: 110 minutes 31.02 seconds (6631.02 seconds total)