Starting phenix.real_space_refine
on Thu Jul 31 03:59:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iyq_35827/07_2025/8iyq_35827_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iyq_35827/07_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_35827/07_2025/8iyq_35827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iyq_35827/07_2025/8iyq_35827.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iyq_35827/07_2025/8iyq_35827_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iyq_35827/07_2025/8iyq_35827_neut.cif"
  }
  resolution = 2.46
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 13.07, per 1000 atoms: 1.00
  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: 3.93
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  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: 5.58
  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: 7.82

  Time building geometry restraints manager: 4.27 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:             1.760
  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:          0.590
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     46.340
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.080
  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:15.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   64.820
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.010   0.001   TRP A 487 
 HIS   0.004   0.001   HIS A 408 
 PHE   0.017   0.001   PHE A 425 
 TYR   0.041   0.001   TYR A 645 
 ARG   0.009   0.000   ARG A1145 

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

*********************** 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  : 1.618 
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: 1.9172
  time to fit residues: 486.0637
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  : 1.496 
-------------------------------------------------------------------------------
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 111 optimal weight:    0.7980
   chunk 100 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0570
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 119 optimal weight:    1.9990
   overall best weight:    0.8500

-------------------------------------------------------------------------------
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 = 0.3857 r_free = 0.3857 target = 0.139929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.112575 restraints weight = 40914.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.75
r_work: 0.3312 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3310
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3310
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13658  Z= 0.204
  Angle     :  0.556   7.004  19086  Z= 0.307
  Chirality :  0.040   0.218   2158
  Planarity :  0.004   0.044   1901
  Dihedral  : 18.814 115.440   3380
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.25), residues: 1195
  helix:  1.44 (0.24), residues: 475
  sheet: -0.89 (0.42), residues: 140
  loop : -0.60 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 487 
 HIS   0.005   0.001   HIS A 529 
 PHE   0.025   0.002   PHE A 425 
 TYR   0.041   0.002   TYR A 645 
 ARG   0.009   0.001   ARG A1410 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05100 (  564)
  hydrogen bonds       : angle       3.94353 ( 1438)
  covalent geometry    : bond        0.00455 (13658)
  covalent geometry    : angle       0.55642 (19086)

*********************** 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
  231 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 218
  time to evaluate  : 1.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 THR cc_start: 0.8794 (m) cc_final: 0.8574 (t)
REVERT: A   41 MET cc_start: 0.7275 (ttp) cc_final: 0.6836 (ttp)
REVERT: A  181 HIS cc_start: 0.7995 (m90) cc_final: 0.7698 (m-70)
REVERT: A  272 LYS cc_start: 0.7928 (ttmm) cc_final: 0.7622 (ttmm)
REVERT: A  374 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7764 (mp0)
REVERT: A  454 GLN cc_start: 0.7188 (tp40) cc_final: 0.6922 (tp40)
REVERT: A  486 ARG cc_start: 0.7929 (ptm-80) cc_final: 0.7587 (ptm-80)
REVERT: A  518 PHE cc_start: 0.8395 (t80) cc_final: 0.8164 (t80)
REVERT: A  550 LYS cc_start: 0.8279 (mmmm) cc_final: 0.8011 (mtmm)
REVERT: A  707 ASP cc_start: 0.7924 (t70) cc_final: 0.7650 (t0)
REVERT: A  970 THR cc_start: 0.7961 (t) cc_final: 0.7653 (m)
REVERT: A  975 ASP cc_start: 0.7456 (m-30) cc_final: 0.7223 (m-30)
REVERT: A  998 ASN cc_start: 0.8101 (t0) cc_final: 0.7889 (t0)
REVERT: A 1000 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8128 (mmmt)
REVERT: A 1005 TRP cc_start: 0.8437 (t-100) cc_final: 0.8112 (t-100)
REVERT: A 1159 MET cc_start: 0.8746 (mtm) cc_final: 0.8538 (mtp)
REVERT: A 1425 ASN cc_start: 0.8325 (m110) cc_final: 0.8012 (m-40)
  outliers start: 13
  outliers final: 10
  residues processed: 226
  average time/residue: 1.5668
  time to fit residues: 380.5854
Evaluate side-chains
  219 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 209
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 LYS
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 1016 VAL
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 116 optimal weight:    0.9990
   chunk 113 optimal weight:    0.7980
   chunk 108 optimal weight:    0.0970
   chunk 45 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 101 optimal weight:    0.0270
   chunk 93 optimal weight:    0.8980
   chunk 122 optimal weight:    1.9990
   overall best weight:    0.5036

-------------------------------------------------------------------------------
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**
** A1009 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 = 0.3876 r_free = 0.3876 target = 0.141393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.114634 restraints weight = 34840.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.32
r_work: 0.3360 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3361
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3361
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13658  Z= 0.147
  Angle     :  0.522   6.004  19086  Z= 0.289
  Chirality :  0.038   0.222   2158
  Planarity :  0.004   0.045   1901
  Dihedral  : 18.705 118.668   3377
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.25 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.24), residues: 1195
  helix:  1.39 (0.24), residues: 477
  sheet: -0.65 (0.44), residues: 134
  loop : -0.65 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 487 
 HIS   0.007   0.001   HIS A 485 
 PHE   0.022   0.001   PHE A 425 
 TYR   0.034   0.001   TYR A 645 
 ARG   0.009   0.001   ARG A1410 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04267 (  564)
  hydrogen bonds       : angle       3.78375 ( 1438)
  covalent geometry    : bond        0.00323 (13658)
  covalent geometry    : angle       0.52151 (19086)

*********************** 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
  238 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 215
  time to evaluate  : 1.435 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 THR cc_start: 0.8726 (m) cc_final: 0.8506 (t)
REVERT: A   41 MET cc_start: 0.7399 (ttp) cc_final: 0.7024 (ttp)
REVERT: A  181 HIS cc_start: 0.7930 (m90) cc_final: 0.7698 (m-70)
REVERT: A  374 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7731 (mp0)
REVERT: A  454 GLN cc_start: 0.7025 (tp40) cc_final: 0.6620 (tp40)
REVERT: A  550 LYS cc_start: 0.8237 (mmmm) cc_final: 0.8026 (mtmm)
REVERT: A  707 ASP cc_start: 0.7901 (t70) cc_final: 0.7618 (t0)
REVERT: A  970 THR cc_start: 0.7956 (t) cc_final: 0.7702 (m)
REVERT: A  975 ASP cc_start: 0.7411 (m-30) cc_final: 0.7175 (m-30)
REVERT: A 1005 TRP cc_start: 0.8460 (t-100) cc_final: 0.8148 (t-100)
REVERT: A 1425 ASN cc_start: 0.8273 (m110) cc_final: 0.7944 (m-40)
  outliers start: 23
  outliers final: 13
  residues processed: 222
  average time/residue: 1.8375
  time to fit residues: 438.4039
Evaluate side-chains
  222 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 209
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
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  148 LYS
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  932 ARG
Chi-restraints excluded: chain A residue 1016 VAL
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 72 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 127 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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**
A 594 ASN
A 998 ASN
** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.139697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.112511 restraints weight = 38884.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.46
r_work: 0.3322 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3323
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3323
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  13658  Z= 0.205
  Angle     :  0.557   5.836  19086  Z= 0.308
  Chirality :  0.040   0.220   2158
  Planarity :  0.004   0.046   1901
  Dihedral  : 18.729 115.363   3377
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.43 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.24), residues: 1195
  helix:  1.19 (0.23), residues: 479
  sheet: -0.35 (0.45), residues: 124
  loop : -0.75 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 487 
 HIS   0.010   0.001   HIS A 485 
 PHE   0.023   0.002   PHE A 425 
 TYR   0.031   0.002   TYR A 645 
 ARG   0.008   0.001   ARG A1410 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04888 (  564)
  hydrogen bonds       : angle       3.86941 ( 1438)
  covalent geometry    : bond        0.00462 (13658)
  covalent geometry    : angle       0.55722 (19086)

*********************** 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
  236 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 214
  time to evaluate  : 1.288 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 THR cc_start: 0.8756 (m) cc_final: 0.8539 (t)
REVERT: A   41 MET cc_start: 0.7428 (ttp) cc_final: 0.7052 (ttp)
REVERT: A  181 HIS cc_start: 0.8045 (m90) cc_final: 0.7771 (m-70)
REVERT: A  272 LYS cc_start: 0.8043 (ttmm) cc_final: 0.7842 (ttmm)
REVERT: A  374 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7749 (mp0)
REVERT: A  517 ASP cc_start: 0.6719 (t70) cc_final: 0.6482 (t70)
REVERT: A  550 LYS cc_start: 0.8263 (mmmm) cc_final: 0.8028 (mtmm)
REVERT: A  707 ASP cc_start: 0.7887 (t70) cc_final: 0.7601 (t0)
REVERT: A  970 THR cc_start: 0.7993 (t) cc_final: 0.7735 (m)
REVERT: A 1000 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8126 (mmmt)
REVERT: A 1005 TRP cc_start: 0.8499 (t-100) cc_final: 0.8207 (t-100)
REVERT: A 1425 ASN cc_start: 0.8354 (m110) cc_final: 0.8000 (m-40)
  outliers start: 22
  outliers final: 17
  residues processed: 222
  average time/residue: 1.5040
  time to fit residues: 359.0737
Evaluate side-chains
  227 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 210
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
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  634 ASP
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 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 80 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 99 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 123 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0980
   chunk 59 optimal weight:    0.4980
   chunk 89 optimal weight:    0.0470
   overall best weight:    0.4878

-------------------------------------------------------------------------------
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**
A 971 GLN
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 = 0.3874 r_free = 0.3874 target = 0.141272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.114867 restraints weight = 36028.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.59
r_work: 0.3354 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13658  Z= 0.141
  Angle     :  0.518   6.899  19086  Z= 0.287
  Chirality :  0.038   0.223   2158
  Planarity :  0.004   0.044   1901
  Dihedral  : 18.671 119.015   3377
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.16 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.24), residues: 1195
  helix:  1.26 (0.24), residues: 478
  sheet: -0.45 (0.44), residues: 130
  loop : -0.70 (0.26), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 641 
 HIS   0.005   0.001   HIS A 651 
 PHE   0.021   0.001   PHE A 425 
 TYR   0.030   0.001   TYR A 645 
 ARG   0.008   0.001   ARG A 507 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04189 (  564)
  hydrogen bonds       : angle       3.77380 ( 1438)
  covalent geometry    : bond        0.00310 (13658)
  covalent geometry    : angle       0.51791 (19086)

*********************** 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
  238 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 214
  time to evaluate  : 1.268 
Fit side-chains
REVERT: A   41 MET cc_start: 0.7364 (ttp) cc_final: 0.6980 (ttp)
REVERT: A  181 HIS cc_start: 0.7958 (m90) cc_final: 0.7711 (m-70)
REVERT: A  269 ASP cc_start: 0.7829 (t0) cc_final: 0.7575 (t0)
REVERT: A  374 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7759 (mp0)
REVERT: A  454 GLN cc_start: 0.7056 (tp40) cc_final: 0.6802 (tp40)
REVERT: A  516 ASP cc_start: 0.7570 (p0) cc_final: 0.7342 (p0)
REVERT: A  550 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7999 (mtmm)
REVERT: A  597 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7122 (mp0)
REVERT: A  707 ASP cc_start: 0.7897 (t70) cc_final: 0.7588 (t0)
REVERT: A  970 THR cc_start: 0.7933 (t) cc_final: 0.7710 (m)
REVERT: A  998 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7888 (t0)
REVERT: A 1005 TRP cc_start: 0.8507 (t-100) cc_final: 0.8224 (t-100)
REVERT: A 1425 ASN cc_start: 0.8338 (m110) cc_final: 0.7993 (m-40)
  outliers start: 24
  outliers final: 17
  residues processed: 225
  average time/residue: 1.7345
  time to fit residues: 419.2398
Evaluate side-chains
  227 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 209
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
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  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  640 LEU
Chi-restraints excluded: chain A residue  932 ARG
Chi-restraints excluded: chain A residue  998 ASN
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1174 LYS
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 124 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0070
   chunk 53 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   overall best weight:    0.7400

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

Flipped N/Q/H residues before XYZ refinement:
A 283 GLN
A 327 GLN
** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.140312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.113292 restraints weight = 37294.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.42
r_work: 0.3336 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3337
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3337
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13658  Z= 0.183
  Angle     :  0.547   8.048  19086  Z= 0.301
  Chirality :  0.039   0.222   2158
  Planarity :  0.004   0.045   1901
  Dihedral  : 18.659 116.987   3377
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 14.34 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.24), residues: 1195
  helix:  1.15 (0.24), residues: 478
  sheet: -0.37 (0.45), residues: 128
  loop : -0.73 (0.26), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 641 
 HIS   0.008   0.001   HIS A 485 
 PHE   0.021   0.002   PHE A 425 
 TYR   0.028   0.002   TYR A 645 
 ARG   0.008   0.001   ARG A 605 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04618 (  564)
  hydrogen bonds       : angle       3.84752 ( 1438)
  covalent geometry    : bond        0.00409 (13658)
  covalent geometry    : angle       0.54749 (19086)

*********************** 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
  235 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 215
  time to evaluate  : 2.003 
Fit side-chains
REVERT: A   12 THR cc_start: 0.8737 (m) cc_final: 0.8511 (t)
REVERT: A   41 MET cc_start: 0.7477 (ttp) cc_final: 0.7109 (ttp)
REVERT: A  181 HIS cc_start: 0.8025 (m90) cc_final: 0.7757 (m-70)
REVERT: A  269 ASP cc_start: 0.7834 (t0) cc_final: 0.7579 (t0)
REVERT: A  272 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7689 (ttmm)
REVERT: A  482 GLU cc_start: 0.7495 (tp30) cc_final: 0.7161 (tp30)
REVERT: A  517 ASP cc_start: 0.6662 (t70) cc_final: 0.6387 (t70)
REVERT: A  550 LYS cc_start: 0.8252 (mmmm) cc_final: 0.8001 (mtmm)
REVERT: A  597 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7275 (mp0)
REVERT: A  707 ASP cc_start: 0.7915 (t70) cc_final: 0.7606 (t0)
REVERT: A  970 THR cc_start: 0.7941 (t) cc_final: 0.7661 (m)
REVERT: A  998 ASN cc_start: 0.8150 (t0) cc_final: 0.7810 (t0)
REVERT: A 1005 TRP cc_start: 0.8486 (t-100) cc_final: 0.8243 (t-100)
REVERT: A 1425 ASN cc_start: 0.8368 (m110) cc_final: 0.8017 (m-40)
  outliers start: 20
  outliers final: 17
  residues processed: 222
  average time/residue: 2.0083
  time to fit residues: 480.7731
Evaluate side-chains
  229 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 212
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
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  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  995 GLN
Chi-restraints excluded: chain A residue 1195 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 59 optimal weight:    0.1980
   chunk 126 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 115 optimal weight:    0.0060
   chunk 72 optimal weight:    0.8980
   chunk 87 optimal weight:    0.8980
   chunk 12 optimal weight:    0.3980
   chunk 24 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
A 235 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 = 0.3885 r_free = 0.3885 target = 0.142039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.115218 restraints weight = 34069.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.30
r_work: 0.3375 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3225
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13658  Z= 0.135
  Angle     :  0.513   7.164  19086  Z= 0.285
  Chirality :  0.037   0.224   2158
  Planarity :  0.004   0.044   1901
  Dihedral  : 18.600 120.163   3377
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 15.34 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.24), residues: 1195
  helix:  1.23 (0.24), residues: 478
  sheet: -0.28 (0.46), residues: 128
  loop : -0.66 (0.26), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 641 
 HIS   0.006   0.001   HIS A 651 
 PHE   0.021   0.001   PHE A 425 
 TYR   0.027   0.001   TYR A 645 
 ARG   0.009   0.001   ARG A1410 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03978 (  564)
  hydrogen bonds       : angle       3.75396 ( 1438)
  covalent geometry    : bond        0.00297 (13658)
  covalent geometry    : angle       0.51325 (19086)

*********************** 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
  234 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 215
  time to evaluate  : 1.337 
Fit side-chains
REVERT: A   41 MET cc_start: 0.7629 (ttp) cc_final: 0.7189 (ttp)
REVERT: A  181 HIS cc_start: 0.8063 (m90) cc_final: 0.7782 (m-70)
REVERT: A  269 ASP cc_start: 0.8068 (t0) cc_final: 0.7764 (t0)
REVERT: A  272 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7887 (ttmm)
REVERT: A  482 GLU cc_start: 0.7696 (tp30) cc_final: 0.7263 (tp30)
REVERT: A  516 ASP cc_start: 0.7796 (p0) cc_final: 0.7544 (p0)
REVERT: A  517 ASP cc_start: 0.6957 (t70) cc_final: 0.6629 (t0)
REVERT: A  550 LYS cc_start: 0.8408 (mmmm) cc_final: 0.8134 (mtmm)
REVERT: A  597 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7590 (mp0)
REVERT: A  970 THR cc_start: 0.7994 (t) cc_final: 0.7666 (p)
REVERT: A  998 ASN cc_start: 0.8308 (t0) cc_final: 0.7986 (t0)
REVERT: A 1005 TRP cc_start: 0.8511 (t-100) cc_final: 0.8265 (t-100)
REVERT: A 1071 MET cc_start: 0.7313 (mtp) cc_final: 0.7021 (mtp)
REVERT: A 1425 ASN cc_start: 0.8526 (m110) cc_final: 0.8193 (m-40)
  outliers start: 19
  outliers final: 18
  residues processed: 221
  average time/residue: 1.5817
  time to fit residues: 375.0819
Evaluate side-chains
  229 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 211
  time to evaluate  : 1.316 
-------------------------------------------------------------------------------
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  309 LYS
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  932 ARG
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  995 GLN
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1174 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 23 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 81 optimal weight:    0.4980
   overall best weight:    0.7982

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.140230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.112256 restraints weight = 47300.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 3.05
r_work: 0.3300 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3297
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3297 r_free = 0.3297    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3297 r_free = 0.3297    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3297
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  13658  Z= 0.194
  Angle     :  0.552   7.731  19086  Z= 0.305
  Chirality :  0.040   0.221   2158
  Planarity :  0.004   0.045   1901
  Dihedral  : 18.623 116.885   3377
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 16.06 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.24), residues: 1195
  helix:  1.14 (0.24), residues: 478
  sheet: -0.35 (0.45), residues: 129
  loop : -0.69 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 641 
 HIS   0.009   0.001   HIS A 485 
 PHE   0.025   0.002   PHE A 518 
 TYR   0.026   0.002   TYR A 645 
 ARG   0.009   0.001   ARG A1410 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04700 (  564)
  hydrogen bonds       : angle       3.84967 ( 1438)
  covalent geometry    : bond        0.00437 (13658)
  covalent geometry    : angle       0.55237 (19086)

*********************** 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
  231 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 215
  time to evaluate  : 3.705 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 THR cc_start: 0.8760 (m) cc_final: 0.8496 (t)
REVERT: A   41 MET cc_start: 0.7505 (ttp) cc_final: 0.7101 (ttp)
REVERT: A  181 HIS cc_start: 0.8067 (m90) cc_final: 0.7792 (m-70)
REVERT: A  269 ASP cc_start: 0.7906 (t0) cc_final: 0.7556 (t0)
REVERT: A  272 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7765 (ttmm)
REVERT: A  517 ASP cc_start: 0.6753 (t70) cc_final: 0.6433 (t0)
REVERT: A  550 LYS cc_start: 0.8311 (mmmm) cc_final: 0.8031 (mtmm)
REVERT: A  597 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7275 (mp0)
REVERT: A  970 THR cc_start: 0.7978 (t) cc_final: 0.7635 (p)
REVERT: A  998 ASN cc_start: 0.8200 (t0) cc_final: 0.7901 (t0)
REVERT: A 1425 ASN cc_start: 0.8443 (m110) cc_final: 0.8096 (m-40)
  outliers start: 16
  outliers final: 17
  residues processed: 219
  average time/residue: 2.4633
  time to fit residues: 581.5746
Evaluate side-chains
  230 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 213
  time to evaluate  : 1.723 
-------------------------------------------------------------------------------
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  309 LYS
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  539 GLU
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 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 52 optimal weight:    0.9980
   chunk 87 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 62 optimal weight:    8.9990
   chunk 53 optimal weight:    0.6980
   chunk 114 optimal weight:    0.9980
   chunk 118 optimal weight:    0.0010
   chunk 47 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 458 ASN
A 485 HIS
A 488 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.141468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.115610 restraints weight = 25677.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.00
r_work: 0.3389 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
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 = 0.11   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 = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13658  Z= 0.153
  Angle     :  0.532   7.646  19086  Z= 0.294
  Chirality :  0.038   0.226   2158
  Planarity :  0.004   0.045   1901
  Dihedral  : 18.569 119.884   3375
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.36 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.79 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.24), residues: 1195
  helix:  1.22 (0.24), residues: 477
  sheet: -0.33 (0.45), residues: 129
  loop : -0.66 (0.26), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 641 
 HIS   0.009   0.001   HIS A 485 
 PHE   0.023   0.001   PHE A 669 
 TYR   0.026   0.001   TYR A 645 
 ARG   0.008   0.001   ARG A 605 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04197 (  564)
  hydrogen bonds       : angle       3.76737 ( 1438)
  covalent geometry    : bond        0.00340 (13658)
  covalent geometry    : angle       0.53157 (19086)

*********************** 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
  227 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 210
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.7628 (ttp) cc_final: 0.7211 (ttp)
REVERT: A  181 HIS cc_start: 0.8054 (m90) cc_final: 0.7795 (m-70)
REVERT: A  269 ASP cc_start: 0.8184 (t0) cc_final: 0.7850 (t0)
REVERT: A  272 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7894 (ttmm)
REVERT: A  482 GLU cc_start: 0.7568 (tp30) cc_final: 0.7251 (tp30)
REVERT: A  516 ASP cc_start: 0.7766 (p0) cc_final: 0.7480 (p0)
REVERT: A  550 LYS cc_start: 0.8346 (mmmm) cc_final: 0.8071 (mtmm)
REVERT: A  597 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7480 (mp0)
REVERT: A  941 ILE cc_start: 0.8443 (mm) cc_final: 0.8225 (tp)
REVERT: A  970 THR cc_start: 0.7993 (t) cc_final: 0.7663 (p)
REVERT: A  998 ASN cc_start: 0.8276 (t0) cc_final: 0.7984 (t0)
REVERT: A 1425 ASN cc_start: 0.8521 (m110) cc_final: 0.8191 (m-40)
  outliers start: 17
  outliers final: 17
  residues processed: 216
  average time/residue: 1.5659
  time to fit residues: 364.0563
Evaluate side-chains
  226 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 209
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
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  309 LYS
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 1016 VAL
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 22 optimal weight:    0.0070
   chunk 53 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 86 optimal weight:    0.0060
   chunk 71 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 21 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.3614

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

Flipped N/Q/H residues before XYZ refinement:
A 477 HIS
A 485 HIS
** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.142387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.116075 restraints weight = 30274.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 2.16
r_work: 0.3399 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3249
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3249
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13658  Z= 0.127
  Angle     :  0.521   7.559  19086  Z= 0.288
  Chirality :  0.037   0.225   2158
  Planarity :  0.004   0.044   1901
  Dihedral  : 18.545 120.778   3375
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.70 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.42 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.24), residues: 1195
  helix:  1.25 (0.24), residues: 478
  sheet: -0.30 (0.45), residues: 129
  loop : -0.63 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 641 
 HIS   0.009   0.001   HIS A 485 
 PHE   0.025   0.001   PHE A 669 
 TYR   0.025   0.001   TYR A 645 
 ARG   0.008   0.001   ARG A 605 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03861 (  564)
  hydrogen bonds       : angle       3.70935 ( 1438)
  covalent geometry    : bond        0.00278 (13658)
  covalent geometry    : angle       0.52102 (19086)

********************** 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
  228 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 213
  time to evaluate  : 1.204 
Fit side-chains
REVERT: A   41 MET cc_start: 0.7554 (ttp) cc_final: 0.7118 (ttp)
REVERT: A   60 GLU cc_start: 0.7591 (mp0) cc_final: 0.7198 (mp0)
REVERT: A  181 HIS cc_start: 0.8028 (m90) cc_final: 0.7750 (m-70)
REVERT: A  269 ASP cc_start: 0.8165 (t0) cc_final: 0.7827 (t0)
REVERT: A  272 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7930 (ttmm)
REVERT: A  482 GLU cc_start: 0.7555 (tp30) cc_final: 0.7284 (tp30)
REVERT: A  517 ASP cc_start: 0.6994 (t70) cc_final: 0.6786 (t70)
REVERT: A  550 LYS cc_start: 0.8420 (mmmm) cc_final: 0.8109 (mtmm)
REVERT: A  597 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7491 (mp0)
REVERT: A  941 ILE cc_start: 0.8415 (mm) cc_final: 0.8172 (tp)
REVERT: A  970 THR cc_start: 0.7964 (t) cc_final: 0.7644 (p)
REVERT: A  998 ASN cc_start: 0.8301 (t0) cc_final: 0.8003 (t0)
REVERT: A 1425 ASN cc_start: 0.8533 (m110) cc_final: 0.8210 (m-40)
  outliers start: 15
  outliers final: 15
  residues processed: 217
  average time/residue: 1.5167
  time to fit residues: 352.9916
Evaluate side-chains
  225 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 210
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
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  932 ARG
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  995 GLN
Chi-restraints excluded: chain A residue 1016 VAL
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 116 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 131 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 130 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 62 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 99 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 ** 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 = 0.3834 r_free = 0.3834 target = 0.138309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.111229 restraints weight = 35023.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.35
r_work: 0.3313 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059  13658  Z= 0.327
  Angle     :  0.646   7.701  19086  Z= 0.351
  Chirality :  0.046   0.226   2158
  Planarity :  0.005   0.053   1901
  Dihedral  : 18.677 114.906   3375
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.37 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 16.79 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.24), residues: 1195
  helix:  0.86 (0.23), residues: 478
  sheet: -0.36 (0.45), residues: 129
  loop : -0.76 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP A 641 
 HIS   0.007   0.002   HIS A 529 
 PHE   0.028   0.002   PHE A 669 
 TYR   0.022   0.002   TYR A 645 
 ARG   0.010   0.001   ARG A 605 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05758 (  564)
  hydrogen bonds       : angle       3.97485 ( 1438)
  covalent geometry    : bond        0.00742 (13658)
  covalent geometry    : angle       0.64553 (19086)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14010.56 seconds
wall clock time: 250 minutes 5.30 seconds (15005.30 seconds total)