Starting phenix.real_space_refine
on Thu Aug  6 08:36:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ehf_48052/08_2026/9ehf_48052.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ehf_48052/08_2026/9ehf_48052.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ehf_48052/08_2026/9ehf_48052.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ehf_48052/08_2026/9ehf_48052.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ehf_48052/08_2026/9ehf_48052.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ehf_48052/08_2026/9ehf_48052.map"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
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: 6
    Type Number    sf(0)   Gaussians
     P     131      5.49       5
     Mg      2      5.21       5
     S      27      5.16       5
     C    8402      2.51       5
     N    2439      2.21       5
     O    2971      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13972
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 11185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1363, 11185
          Classifications: {'peptide': 1363}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 36, 'TRANS': 1326}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 58
          Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 20
    Chain: "B"
      Number of atoms: 1987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 1987
          Classifications: {'RNA': 94}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 39, 'rna3p_pyr': 43}
          Link IDs: {'rna2p': 11, 'rna3p': 82}
    Chain: "C"
      Number of atoms: 242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 242
          Classifications: {'DNA': 12}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 11}
    Chain: "D"
      Number of atoms: 186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 186
          Classifications: {'DNA': 9}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 8}
    Chain: "c"
      Number of atoms: 370
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 370
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.14, per 1000 atoms: 0.22
  Number of scatterers: 13972
  At special positions: 0
  Unit cell: (88.3192, 110.816, 142.477, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      27     16.00
     P     131     15.00
     Mg      2     11.99
     O    2971      8.00
     N    2439      7.00
     C    8402      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 537.8 milliseconds
  

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2612

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 12 sheets defined
      51.4% alpha, 11.4% beta
      52 base pairs and 92 stacking pairs defined.
    Time for finding SS restraints: 1.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 33
      removed outlier: 3.856A  pdb=" N   LEU A  33 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 82
      removed outlier: 3.840A  pdb=" N   LYS A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 100
    Processing helix  chain 'A' and resid 311 through 324
    Processing helix  chain 'A' and resid 330 through 342
    Processing helix  chain 'A' and resid 349 through 362
    Processing helix  chain 'A' and resid 364 through 373
      removed outlier: 3.887A  pdb=" N   LEU A 368 " --> pdb=" O   GLU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 378
    Processing helix  chain 'A' and resid 384 through 398
    Processing helix  chain 'A' and resid 416 through 431
      removed outlier: 3.517A  pdb=" N   GLN A 426 " --> pdb=" O   ASN A 422 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   THR A 429 " --> pdb=" O   LYS A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 438
    Processing helix  chain 'A' and resid 466 through 474
    Processing helix  chain 'A' and resid 476 through 486
    Processing helix  chain 'A' and resid 487 through 495
    Processing helix  chain 'A' and resid 496 through 503
    Processing helix  chain 'A' and resid 520 through 525
      removed outlier: 3.728A  pdb=" N   SER A 525 " --> pdb=" O   GLN A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 543
      removed outlier: 3.516A  pdb=" N   LEU A 533 " --> pdb=" O   ASP A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 566
    Processing helix  chain 'A' and resid 579 through 587
    Processing helix  chain 'A' and resid 606 through 623
    Processing helix  chain 'A' and resid 649 through 652
    Processing helix  chain 'A' and resid 663 through 666
    Processing helix  chain 'A' and resid 667 through 677
    Processing helix  chain 'A' and resid 679 through 688
    Processing helix  chain 'A' and resid 691 through 703
    Processing helix  chain 'A' and resid 705 through 721
    Processing helix  chain 'A' and resid 723 through 734
    Processing helix  chain 'A' and resid 739 through 750
    Processing helix  chain 'A' and resid 762 through 773
    Processing helix  chain 'A' and resid 779 through 789
      removed outlier: 3.807A  pdb=" N   LYS A 789 " --> pdb=" O   ARG A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 792 through 804
    Processing helix  chain 'A' and resid 814 through 824
    Processing helix  chain 'A' and resid 860 through 887
      removed outlier: 5.013A  pdb=" N   GLN A 879 " --> pdb=" O   ASP A 875 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   ASN A 880 " --> pdb=" O   ASP A 876 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 935 through 944
    Processing helix  chain 'A' and resid 983 through 985
      No H-bonds generated for 'chain 'A' and resid 983 through 985'
    Processing helix  chain 'A' and resid 991 through 999
    Processing helix  chain 'A' and resid 1004 through 1008
    Processing helix  chain 'A' and resid 1009 through 1018
    Processing helix  chain 'A' and resid 1021 through 1034
    Processing helix  chain 'A' and resid 1053 through 1063
    Processing helix  chain 'A' and resid 1064 through 1066
      No H-bonds generated for 'chain 'A' and resid 1064 through 1066'
    Processing helix  chain 'A' and resid 1070 through 1081
    Processing helix  chain 'A' and resid 1082 through 1087
    Processing helix  chain 'A' and resid 1091 through 1110
    Processing helix  chain 'A' and resid 1113 through 1115
      No H-bonds generated for 'chain 'A' and resid 1113 through 1115'
    Processing helix  chain 'A' and resid 1127 through 1131
    Processing helix  chain 'A' and resid 1132 through 1144
    Processing helix  chain 'A' and resid 1144 through 1150
    Processing helix  chain 'A' and resid 1159 through 1177
      removed outlier: 3.842A  pdb=" N   LEU A1163 " --> pdb=" O   SER A1159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1208 through 1213
    Processing helix  chain 'A' and resid 1282 through 1292
    Processing helix  chain 'A' and resid 1293 through 1296
      removed outlier: 3.543A  pdb=" N   VAL A1296 " --> pdb=" O   LEU A1293 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1293 through 1296'
    Processing helix  chain 'A' and resid 1308 through 1319
      removed outlier: 3.740A  pdb=" N   LEU A1312 " --> pdb=" O   THR A1308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1333 through 1346
      removed outlier: 3.746A  pdb=" N   ASN A1346 " --> pdb=" O   ILE A1342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1347 through 1350
    Processing helix  chain 'A' and resid 1355 through 1364
    Processing helix  chain 'A' and resid 1375 through 1384
    Processing helix  chain 'A' and resid 1385 through 1388
    Processing helix  chain 'A' and resid 1398 through 1410
    Processing helix  chain 'A' and resid 1416 through 1425
    Processing helix  chain 'A' and resid 1472 through 1476
    Processing helix  chain 'A' and resid 1536 through 1543
    Processing helix  chain 'A' and resid 1569 through 1579
    Processing helix  chain 'A' and resid 1586 through 1595
    Processing helix  chain 'A' and resid 1608 through 1624
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25
    Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 25
      removed outlier: 9.640A  pdb=" N   SER A1220 " --> pdb=" O   LYS A  36 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   GLY A  38 " --> pdb=" O   SER A1220 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   LYS A1222 " --> pdb=" O   GLY A  38 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   VAL A  40 " --> pdb=" O   LYS A1222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 465
    Processing sheet with id=AA4, first strand: chain 'A' and resid 597 through 598
    Processing sheet with id=AA5, first strand: chain 'A' and resid 630 through 635
      removed outlier: 7.590A  pdb=" N   GLU A 631 " --> pdb=" O   THR A 644 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 966 through 969
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1441 through 1446
      removed outlier: 4.690A  pdb=" N   PHE A1441 " --> pdb=" O   ILE A1373 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU A1443 " --> pdb=" O   VAL A1371 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ARG A1370 " --> pdb=" O   ILE A1244 " (cutoff:3.500A)
      removed outlier: 8.841A  pdb=" N   ILE A1244 " --> pdb=" O   ARG A1370 " (cutoff:3.500A)
      removed outlier: 13.744A  pdb=" N   LYS A1372 " --> pdb=" O   ASP A1242 " (cutoff:3.500A)
      removed outlier: 17.962A  pdb=" N   ASP A1242 " --> pdb=" O   LYS A1372 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   GLY A1243 " --> pdb=" O   ASN A1469 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ASN A1469 " --> pdb=" O   GLY A1243 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ILE A1467 " --> pdb=" O   TYR A1245 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   GLU A1247 " --> pdb=" O   TYR A1465 " (cutoff:3.500A)
      removed outlier: 10.883A  pdb=" N   TYR A1465 " --> pdb=" O   GLU A1247 " (cutoff:3.500A)
      removed outlier: 18.133A  pdb=" N   TYR A1249 " --> pdb=" O   PHE A1463 " (cutoff:3.500A)
      removed outlier: 22.719A  pdb=" N   PHE A1463 " --> pdb=" O   TYR A1249 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1270 through 1273
      removed outlier: 4.663A  pdb=" N   VAL A1261 " --> pdb=" O   ILE A1273 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1276 through 1277
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1390 through 1391
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1491 through 1496
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1530 through 1533
      removed outlier: 4.078A  pdb=" N   ILE A1547 " --> pdb=" O   VAL A1533 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR A1546 " --> pdb=" O   LYS A1562 " (cutoff:3.500A)

    532 hydrogen bonds defined for protein.
    1521 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      131 hydrogen bonds
      246 hydrogen bond angles
      0 basepair planarities
      52 basepair parallelities
      92 stacking parallelities
  Total time for adding SS restraints: 3.67

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3352
        1.33 -     1.46: 3797
        1.46 -     1.58: 7068
        1.58 -     1.70: 260
        1.70 -     1.82: 38
  Bond restraints: 14515
  Sorted by residual:
  bond pdb=" C3'  DC C   1 "
       pdb=" C2'  DC C   1 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 8.00e-03 1.56e+04 1.82e+01
  bond pdb=" C3'  DG D   3 "
       pdb=" O3'  DG D   3 "
    ideal  model  delta    sigma   weight residual
    1.435  1.488 -0.053 1.30e-02 5.92e+03 1.66e+01
  bond pdb=" C1'  DC c  24 "
       pdb=" N1   DC c  24 "
    ideal  model  delta    sigma   weight residual
    1.468  1.515 -0.047 1.40e-02 5.10e+03 1.14e+01
  bond pdb=" C3'  DG C   3 "
       pdb=" O3'  DG C   3 "
    ideal  model  delta    sigma   weight residual
    1.435  1.396  0.039 1.30e-02 5.92e+03 9.03e+00
  bond pdb=" C5'  DG C  12 "
       pdb=" C4'  DG C  12 "
    ideal  model  delta    sigma   weight residual
    1.512  1.532 -0.020 7.00e-03 2.04e+04 8.16e+00
  ... (remaining 14510 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.29: 19951
        3.29 -     6.58: 194
        6.58 -     9.88: 22
        9.88 -    13.17: 2
       13.17 -    16.46: 3
  Bond angle restraints: 20172
  Sorted by residual:
  angle pdb=" O4'  DA C  11 "
        pdb=" C1'  DA C  11 "
        pdb=" N9   DA C  11 "
      ideal   model   delta    sigma   weight residual
     108.00  112.55   -4.55 7.00e-01 2.04e+00 4.22e+01
  angle pdb=" C3'  DG D   3 "
        pdb=" O3'  DG D   3 "
        pdb=" P    DT D   4 "
      ideal   model   delta    sigma   weight residual
     119.70  126.66   -6.96 1.20e+00 6.94e-01 3.37e+01
  angle pdb=" O5'   C B  18 "
        pdb=" C5'   C B  18 "
        pdb=" C4'   C B  18 "
      ideal   model   delta    sigma   weight residual
     109.40  114.02   -4.62 8.00e-01 1.56e+00 3.34e+01
  angle pdb=" C2    C B  34 "
        pdb=" N1    C B  34 "
        pdb=" C6    C B  34 "
      ideal   model   delta    sigma   weight residual
     120.30  118.05    2.25 4.00e-01 6.25e+00 3.18e+01
  angle pdb=" CB  MET A 629 "
        pdb=" CG  MET A 629 "
        pdb=" SD  MET A 629 "
      ideal   model   delta    sigma   weight residual
     112.70  129.16  -16.46 3.00e+00 1.11e-01 3.01e+01
  ... (remaining 20167 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.64: 8276
       32.64 -    65.28: 491
       65.28 -    97.92: 51
       97.92 -   130.56: 1
      130.56 -   163.19: 1
  Dihedral angle restraints: 8820
    sinusoidal: 4790
      harmonic: 4030
  Sorted by residual:
  dihedral pdb=" CA  ASN A 453 "
           pdb=" C   ASN A 453 "
           pdb=" N   ASN A 454 "
           pdb=" CA  ASN A 454 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.77  -27.23     0      5.00e+00 4.00e-02 2.97e+01
  dihedral pdb=" CA  TYR A 449 "
           pdb=" C   TYR A 449 "
           pdb=" N   LEU A 450 "
           pdb=" CA  LEU A 450 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.90  -27.10     0      5.00e+00 4.00e-02 2.94e+01
  dihedral pdb=" CA  ASP A 957 "
           pdb=" C   ASP A 957 "
           pdb=" N   GLY A 958 "
           pdb=" CA  GLY A 958 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.48  -26.52     0      5.00e+00 4.00e-02 2.81e+01
  ... (remaining 8817 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1399
       0.045 -    0.091: 564
       0.091 -    0.136: 229
       0.136 -    0.181: 70
       0.181 -    0.226: 15
  Chirality restraints: 2277
  Sorted by residual:
  chirality pdb=" C1'   A B  51 "
            pdb=" O4'   A B  51 "
            pdb=" C2'   A B  51 "
            pdb=" N9    A B  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.24    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" C1'   C B  34 "
            pdb=" O4'   C B  34 "
            pdb=" C2'   C B  34 "
            pdb=" N1    C B  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.25    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" C1'   A B  86 "
            pdb=" O4'   A B  86 "
            pdb=" C2'   A B  86 "
            pdb=" N9    A B  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.22    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 2274 not shown)

  Planarity restraints: 2113
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 824 "    0.439 9.50e-02 1.11e+02   1.98e-01 2.96e+01
        pdb=" NE  ARG A 824 "   -0.040 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 824 "    0.037 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 824 "   -0.017 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 824 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1006 "   -0.316 9.50e-02 1.11e+02   1.43e-01 1.61e+01
        pdb=" NE  ARG A1006 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1006 "   -0.030 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1006 "    0.014 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1006 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 310 "   -0.313 9.50e-02 1.11e+02   1.41e-01 1.51e+01
        pdb=" NE  ARG A 310 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 310 "   -0.027 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 310 "    0.013 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 310 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2110 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 7236
        3.02 -     3.49: 13869
        3.49 -     3.96: 25603
        3.96 -     4.43: 29718
        4.43 -     4.90: 42960
  Nonbonded interactions: 119386
  Sorted by model distance:
  nonbonded pdb=" O4'   C B  18 "
            pdb=" C6    C B  18 "
     model   vdw
     2.549 2.672
  nonbonded pdb=" O5'  DG C   3 "
            pdb=" O4'  DG C   3 "
     model   vdw
     2.549 2.432
  nonbonded pdb=" N1    G B  11 "
            pdb=" C4    G B  11 "
     model   vdw
     2.584 2.672
  nonbonded pdb=" N1    G B  62 "
            pdb=" C4    G B  62 "
     model   vdw
     2.587 2.672
  nonbonded pdb=" N1    G B  31 "
            pdb=" C4    G B  31 "
     model   vdw
     2.589 2.672
  ... (remaining 119381 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             9.110
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.030
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:6.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
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      :  0.005   0.071  14515  Z= 0.337
  Angle     :  0.966  16.460  20172  Z= 0.661
  Chirality :  0.061   0.226   2277
  Planarity :  0.011   0.198   2113
  Dihedral  : 18.250 163.195   6208
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 1.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 12.82 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.22), residues: 1349
  helix: -0.10 (0.19), residues: 635
  sheet: -0.12 (0.38), residues: 161
  loop :  0.29 (0.28), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.042   0.004   ARG A 824 
 TYR   0.026   0.003   TYR A1194 
 PHE   0.040   0.002   PHE A 783 
 TRP   0.029   0.003   TRP A1459 
 HIS   0.007   0.001   HIS A1177 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00527 /  0.34 (14515)
  covalent geometry    : angle       0.96607 /  0.66 (20172)
  hydrogen bonds       : bond        0.12389 /  8.43 (  659)
  hydrogen bonds       : angle       5.97710 /  4.26 ( 1767)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.465 
Fit side-chains
REVERT: A   89 LYS cc_start: 0.7984 (mmpt) cc_final: 0.7615 (mtmm)
REVERT: A  418 LYS cc_start: 0.7295 (tppt) cc_final: 0.6761 (mptt)
REVERT: A  515 GLU cc_start: 0.8653 (tt0) cc_final: 0.8264 (tm-30)
REVERT: A  555 GLU cc_start: 0.8519 (tp30) cc_final: 0.8194 (tp30)
REVERT: A  806 GLU cc_start: 0.8457 (tt0) cc_final: 0.7690 (mp0)
REVERT: A  898 GLU cc_start: 0.8028 (tt0) cc_final: 0.7593 (pp20)
REVERT: A 1006 ARG cc_start: 0.7802 (mtt90) cc_final: 0.7104 (mtm-85)
REVERT: A 1068 ASP cc_start: 0.7092 (m-30) cc_final: 0.6645 (t0)
REVERT: A 1268 LYS cc_start: 0.8774 (mtmm) cc_final: 0.8484 (mppt)
REVERT: A 1358 MET cc_start: 0.8836 (tpt) cc_final: 0.8439 (tpt)
  outliers start: 6
  outliers final: 4
  residues processed: 92
  average time/residue: 0.6048
  time to fit residues: 61.5829
Evaluate side-chains
  84 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue 1207 ASP
Chi-restraints excluded: chain A residue 1240 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.0010
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.7386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 604 GLN
A 670 ASN
A 702 HIS
A 938 ASN
A1129 ASN
A1148 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.113814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.090879 restraints weight = 21448.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.98
r_work: 0.3170 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.0839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14515  Z= 0.167
  Angle     :  0.568   7.288  20172  Z= 0.323
  Chirality :  0.042   0.282   2277
  Planarity :  0.004   0.034   2113
  Dihedral  : 18.477 167.758   3361
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 11.42 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.23), residues: 1349
  helix:  0.97 (0.20), residues: 636
  sheet:  0.23 (0.41), residues: 144
  loop :  0.60 (0.27), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  32 
 TYR   0.013   0.002   TYR A1265 
 PHE   0.019   0.002   PHE A 783 
 TRP   0.014   0.002   TRP A 698 
 HIS   0.004   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.17 (14515)
  covalent geometry    : angle       0.56766 /  0.32 (20172)
  hydrogen bonds       : bond        0.04971 /  3.24 (  659)
  hydrogen bonds       : angle       4.70604 /  3.36 ( 1767)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7513 (tp30)
REVERT: A  407 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8117 (mp10)
REVERT: A  418 LYS cc_start: 0.7302 (tppt) cc_final: 0.6811 (ttmm)
REVERT: A  515 GLU cc_start: 0.8657 (tt0) cc_final: 0.8244 (tm-30)
REVERT: A  898 GLU cc_start: 0.8002 (tt0) cc_final: 0.7295 (pp20)
REVERT: A  942 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7778 (mm-30)
REVERT: A 1006 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7352 (mtm-85)
REVERT: A 1268 LYS cc_start: 0.8818 (mtmm) cc_final: 0.8553 (mppt)
REVERT: A 1358 MET cc_start: 0.8843 (tpt) cc_final: 0.8421 (tpt)
  outliers start: 20
  outliers final: 7
  residues processed: 101
  average time/residue: 0.5703
  time to fit residues: 63.6231
Evaluate side-chains
  84 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  685 ASP
Chi-restraints excluded: chain A residue  704 ARG
Chi-restraints excluded: chain A residue  855 THR
Chi-restraints excluded: chain A residue 1307 SER
Chi-restraints excluded: chain A residue 1622 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 100 optimal weight:    0.1980
   chunk 115 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  53 ASN
A 604 GLN
A 659 HIS
A 931 ASN
A1082 ASN
A1148 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.113480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.090312 restraints weight = 21438.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.01
r_work: 0.3161 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.1088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14515  Z= 0.148
  Angle     :  0.528   7.627  20172  Z= 0.302
  Chirality :  0.041   0.302   2277
  Planarity :  0.003   0.035   2113
  Dihedral  : 18.229 167.246   3355
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.83 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.23), residues: 1349
  helix:  1.23 (0.20), residues: 636
  sheet: -0.04 (0.40), residues: 154
  loop :  0.73 (0.28), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1078 
 TYR   0.011   0.001   TYR A1265 
 PHE   0.015   0.001   PHE A1420 
 TRP   0.012   0.001   TRP A  79 
 HIS   0.004   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.15 (14515)
  covalent geometry    : angle       0.52825 /  0.30 (20172)
  hydrogen bonds       : bond        0.04719 /  3.04 (  659)
  hydrogen bonds       : angle       4.59822 /  3.26 ( 1767)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 84
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7476 (tp30)
REVERT: A  407 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8123 (mp10)
REVERT: A  418 LYS cc_start: 0.7317 (tppt) cc_final: 0.6874 (ttmm)
REVERT: A  515 GLU cc_start: 0.8637 (tt0) cc_final: 0.8224 (tm-30)
REVERT: A  898 GLU cc_start: 0.7983 (tt0) cc_final: 0.7281 (pp20)
REVERT: A  942 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7843 (mm-30)
REVERT: A 1006 ARG cc_start: 0.7867 (mtt90) cc_final: 0.7366 (mtm-85)
REVERT: A 1268 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8566 (mppt)
REVERT: A 1550 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8044 (ttpp)
REVERT: A 1552 ASP cc_start: 0.8998 (p0) cc_final: 0.8710 (p0)
  outliers start: 27
  outliers final: 9
  residues processed: 105
  average time/residue: 0.5722
  time to fit residues: 66.6497
Evaluate side-chains
  91 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  704 ARG
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  855 THR
Chi-restraints excluded: chain A residue 1307 SER
Chi-restraints excluded: chain A residue 1550 LYS
Chi-restraints excluded: chain A residue 1622 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 120 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 114 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 145 optimal weight:    5.9990
   chunk 27 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9980
   chunk 93 optimal weight:    4.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 604 GLN
A 931 ASN
A1148 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.112149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.088977 restraints weight = 21579.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.99
r_work: 0.3137 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14515  Z= 0.170
  Angle     :  0.537   8.715  20172  Z= 0.302
  Chirality :  0.041   0.307   2277
  Planarity :  0.004   0.036   2113
  Dihedral  : 18.189 166.639   3355
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.16 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.23), residues: 1349
  helix:  1.38 (0.20), residues: 636
  sheet: -0.15 (0.40), residues: 154
  loop :  0.69 (0.28), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1078 
 TYR   0.012   0.001   TYR A1265 
 PHE   0.015   0.002   PHE A1420 
 TRP   0.012   0.002   TRP A  79 
 HIS   0.006   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.17 (14515)
  covalent geometry    : angle       0.53669 /  0.30 (20172)
  hydrogen bonds       : bond        0.04662 /  3.01 (  659)
  hydrogen bonds       : angle       4.48122 /  3.17 ( 1767)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 86
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7484 (tp30)
REVERT: A  407 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8171 (mp10)
REVERT: A  418 LYS cc_start: 0.7352 (tppt) cc_final: 0.6895 (ttmm)
REVERT: A  488 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7994 (tm-30)
REVERT: A  491 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7300 (mp-120)
REVERT: A  515 GLU cc_start: 0.8664 (tt0) cc_final: 0.8242 (tm-30)
REVERT: A  771 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6805 (mp)
REVERT: A  898 GLU cc_start: 0.7969 (tt0) cc_final: 0.7236 (OUTLIER)
REVERT: A  938 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7572 (m-40)
REVERT: A  942 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7821 (mm-30)
REVERT: A 1006 ARG cc_start: 0.7872 (mtt90) cc_final: 0.7350 (mtm-85)
REVERT: A 1358 MET cc_start: 0.8843 (tpt) cc_final: 0.8456 (tpt)
REVERT: A 1540 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.8009 (mmm160)
REVERT: A 1550 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.7971 (ttpp)
REVERT: A 1552 ASP cc_start: 0.9022 (p0) cc_final: 0.8756 (p0)
  outliers start: 29
  outliers final: 12
  residues processed: 109
  average time/residue: 0.5614
  time to fit residues: 67.9113
Evaluate side-chains
  99 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  491 GLN
Chi-restraints excluded: chain A residue  704 ARG
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  823 HIS
Chi-restraints excluded: chain A residue  855 THR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1011 ASN
Chi-restraints excluded: chain A residue 1307 SER
Chi-restraints excluded: chain A residue 1550 LYS
Chi-restraints excluded: chain A residue 1622 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 129 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 139 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 138 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  53 ASN
A 604 GLN
A1148 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.111468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.088239 restraints weight = 21616.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.01
r_work: 0.3121 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14515  Z= 0.177
  Angle     :  0.534   9.262  20172  Z= 0.301
  Chirality :  0.041   0.307   2277
  Planarity :  0.004   0.038   2113
  Dihedral  : 18.179 166.480   3355
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.83 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.23), residues: 1349
  helix:  1.43 (0.20), residues: 637
  sheet: -0.24 (0.38), residues: 164
  loop :  0.63 (0.28), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1078 
 TYR   0.012   0.001   TYR A1265 
 PHE   0.016   0.002   PHE A1420 
 TRP   0.012   0.002   TRP A  79 
 HIS   0.006   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.18 (14515)
  covalent geometry    : angle       0.53425 /  0.30 (20172)
  hydrogen bonds       : bond        0.04665 /  3.01 (  659)
  hydrogen bonds       : angle       4.41703 /  3.12 ( 1767)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 90
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7486 (tp30)
REVERT: A  407 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7879 (mp10)
REVERT: A  418 LYS cc_start: 0.7351 (tppt) cc_final: 0.6895 (ttmm)
REVERT: A  488 GLN cc_start: 0.8366 (tm-30) cc_final: 0.8090 (tm-30)
REVERT: A  515 GLU cc_start: 0.8635 (tt0) cc_final: 0.8215 (tm-30)
REVERT: A  555 GLU cc_start: 0.8504 (tp30) cc_final: 0.8230 (tp30)
REVERT: A  708 LYS cc_start: 0.7571 (tttt) cc_final: 0.6971 (tmtm)
REVERT: A  771 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6791 (mp)
REVERT: A  898 GLU cc_start: 0.7950 (tt0) cc_final: 0.7214 (OUTLIER)
REVERT: A  938 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7558 (m-40)
REVERT: A  942 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7805 (mm-30)
REVERT: A 1006 ARG cc_start: 0.7904 (mtt90) cc_final: 0.7369 (mtm-85)
REVERT: A 1540 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7894 (mmm160)
REVERT: A 1550 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.7971 (ttpp)
REVERT: A 1552 ASP cc_start: 0.9032 (p0) cc_final: 0.8771 (p0)
  outliers start: 33
  outliers final: 15
  residues processed: 116
  average time/residue: 0.5155
  time to fit residues: 66.7787
Evaluate side-chains
  104 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  704 ARG
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  823 HIS
Chi-restraints excluded: chain A residue  855 THR
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1011 ASN
Chi-restraints excluded: chain A residue 1210 SER
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1307 SER
Chi-restraints excluded: chain A residue 1550 LYS
Chi-restraints excluded: chain A residue 1622 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 137 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 127 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0870
   chunk 5 optimal weight:    0.6980
   chunk 110 optimal weight:    1.9990
   overall best weight:    0.7360

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 491 GLN
A 604 GLN
A 798 GLN
A 931 ASN
A1148 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.111743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.088663 restraints weight = 21415.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 1.99
r_work: 0.3132 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14515  Z= 0.155
  Angle     :  0.516  10.313  20172  Z= 0.292
  Chirality :  0.040   0.305   2277
  Planarity :  0.003   0.038   2113
  Dihedral  : 18.166 166.763   3355
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 12.49 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.23), residues: 1349
  helix:  1.53 (0.20), residues: 637
  sheet: -0.20 (0.38), residues: 164
  loop :  0.62 (0.28), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1078 
 TYR   0.012   0.001   TYR A1265 
 PHE   0.015   0.001   PHE A1420 
 TRP   0.013   0.001   TRP A  79 
 HIS   0.005   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 (14515)
  covalent geometry    : angle       0.51636 /  0.29 (20172)
  hydrogen bonds       : bond        0.04442 /  2.85 (  659)
  hydrogen bonds       : angle       4.35865 /  3.07 ( 1767)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 88
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7468 (tp30)
REVERT: A  407 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8271 (mp10)
REVERT: A  418 LYS cc_start: 0.7347 (tppt) cc_final: 0.6894 (ttmm)
REVERT: A  488 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8075 (tm-30)
REVERT: A  515 GLU cc_start: 0.8652 (tt0) cc_final: 0.8206 (tm-30)
REVERT: A  555 GLU cc_start: 0.8484 (tp30) cc_final: 0.8194 (tp30)
REVERT: A  708 LYS cc_start: 0.7567 (tttt) cc_final: 0.6967 (tmtm)
REVERT: A  771 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6750 (mp)
REVERT: A  898 GLU cc_start: 0.7962 (tt0) cc_final: 0.7221 (OUTLIER)
REVERT: A  938 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7521 (m-40)
REVERT: A  942 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7780 (mm-30)
REVERT: A 1358 MET cc_start: 0.8837 (tpt) cc_final: 0.8467 (tpt)
REVERT: A 1540 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.7789 (mmm160)
REVERT: A 1550 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7958 (ttpp)
REVERT: A 1552 ASP cc_start: 0.9034 (p0) cc_final: 0.8757 (p0)
  outliers start: 36
  outliers final: 14
  residues processed: 115
  average time/residue: 0.5137
  time to fit residues: 66.0451
Evaluate side-chains
  104 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  823 HIS
Chi-restraints excluded: chain A residue  855 THR
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1011 ASN
Chi-restraints excluded: chain A residue 1210 SER
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1550 LYS
Chi-restraints excluded: chain A residue 1622 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 125 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 114 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0770
   chunk 64 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 135 optimal weight:    0.7980
   chunk 122 optimal weight:    0.7980
   chunk 92 optimal weight:    4.9990
   overall best weight:    0.6738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  53 ASN
A 491 GLN
A 604 GLN
A 798 GLN
A 931 ASN
A1148 GLN
A1287 ASN
A1515 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.111967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.088954 restraints weight = 21360.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.99
r_work: 0.3136 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14515  Z= 0.147
  Angle     :  0.508   8.377  20172  Z= 0.288
  Chirality :  0.040   0.301   2277
  Planarity :  0.003   0.037   2113
  Dihedral  : 18.138 166.886   3355
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.06 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.23), residues: 1349
  helix:  1.60 (0.20), residues: 637
  sheet: -0.21 (0.38), residues: 164
  loop :  0.62 (0.28), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1078 
 TYR   0.014   0.001   TYR A 449 
 PHE   0.015   0.001   PHE A1420 
 TRP   0.012   0.001   TRP A  79 
 HIS   0.005   0.001   HIS A  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.15 (14515)
  covalent geometry    : angle       0.50792 /  0.29 (20172)
  hydrogen bonds       : bond        0.04347 /  2.79 (  659)
  hydrogen bonds       : angle       4.28858 /  3.02 ( 1767)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 87
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7449 (tp30)
REVERT: A  407 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8286 (mp10)
REVERT: A  418 LYS cc_start: 0.7339 (tppt) cc_final: 0.6889 (ttmm)
REVERT: A  450 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8391 (mp)
REVERT: A  488 GLN cc_start: 0.8343 (tm-30) cc_final: 0.8022 (tm-30)
REVERT: A  515 GLU cc_start: 0.8668 (tt0) cc_final: 0.8214 (tm-30)
REVERT: A  555 GLU cc_start: 0.8478 (tp30) cc_final: 0.8174 (tp30)
REVERT: A  771 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6734 (mp)
REVERT: A  898 GLU cc_start: 0.7929 (tt0) cc_final: 0.7215 (OUTLIER)
REVERT: A  938 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7509 (m-40)
REVERT: A  942 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7744 (mm-30)
REVERT: A 1268 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8587 (mppt)
REVERT: A 1358 MET cc_start: 0.8841 (tpt) cc_final: 0.8439 (tpt)
REVERT: A 1540 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7791 (mmm160)
REVERT: A 1550 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7931 (ttpp)
REVERT: A 1552 ASP cc_start: 0.9038 (p0) cc_final: 0.8762 (p0)
  outliers start: 29
  outliers final: 14
  residues processed: 110
  average time/residue: 0.4868
  time to fit residues: 59.4683
Evaluate side-chains
  104 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  823 HIS
Chi-restraints excluded: chain A residue  855 THR
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  900 ASN
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1210 SER
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1550 LYS
Chi-restraints excluded: chain A residue 1622 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 131 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0170
   chunk 92 optimal weight:    5.9990
   chunk 132 optimal weight:    0.5980
   chunk 86 optimal weight:    0.2980
   chunk 125 optimal weight:    0.0070
   chunk 15 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.3036

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  60 HIS
A 491 GLN
A 604 GLN
** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 798 GLN
A 931 ASN
A1148 GLN
A1515 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.114472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.091632 restraints weight = 21344.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.00
r_work: 0.3182 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  14515  Z= 0.108
  Angle     :  0.483  12.377  20172  Z= 0.275
  Chirality :  0.038   0.292   2277
  Planarity :  0.003   0.038   2113
  Dihedral  : 18.090 167.648   3355
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.64 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.23), residues: 1349
  helix:  1.74 (0.20), residues: 638
  sheet: -0.14 (0.40), residues: 154
  loop :  0.64 (0.28), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1078 
 TYR   0.012   0.001   TYR A1160 
 PHE   0.015   0.001   PHE A1420 
 TRP   0.014   0.001   TRP A  79 
 HIS   0.003   0.000   HIS A1177 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00212 /  0.11 (14515)
  covalent geometry    : angle       0.48276 /  0.28 (20172)
  hydrogen bonds       : bond        0.03928 /  2.50 (  659)
  hydrogen bonds       : angle       4.15125 /  2.92 ( 1767)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7391 (tp30)
REVERT: A  407 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8212 (mp10)
REVERT: A  418 LYS cc_start: 0.7352 (tppt) cc_final: 0.6912 (ttmm)
REVERT: A  450 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8363 (mp)
REVERT: A  454 ASN cc_start: 0.8002 (t0) cc_final: 0.7756 (t0)
REVERT: A  488 GLN cc_start: 0.8330 (tm-30) cc_final: 0.8006 (tm-30)
REVERT: A  515 GLU cc_start: 0.8700 (tt0) cc_final: 0.8247 (tm-30)
REVERT: A  555 GLU cc_start: 0.8502 (tp30) cc_final: 0.8233 (tp30)
REVERT: A  898 GLU cc_start: 0.7907 (tt0) cc_final: 0.7217 (OUTLIER)
REVERT: A  938 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7379 (m-40)
REVERT: A  942 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7739 (mm-30)
REVERT: A 1268 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8613 (mppt)
REVERT: A 1358 MET cc_start: 0.8814 (tpt) cc_final: 0.8403 (tpt)
REVERT: A 1439 LYS cc_start: 0.8612 (mttt) cc_final: 0.8376 (mmtp)
REVERT: A 1540 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.7871 (mmm160)
REVERT: A 1550 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.7877 (ttpp)
REVERT: A 1552 ASP cc_start: 0.9030 (p0) cc_final: 0.8770 (p0)
  outliers start: 28
  outliers final: 12
  residues processed: 123
  average time/residue: 0.5584
  time to fit residues: 76.2411
Evaluate side-chains
  109 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  823 HIS
Chi-restraints excluded: chain A residue  855 THR
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1210 SER
Chi-restraints excluded: chain A residue 1240 THR
Chi-restraints excluded: chain A residue 1550 LYS
Chi-restraints excluded: chain A residue 1622 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 142 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   chunk 132 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  53 ASN
A 491 GLN
A 604 GLN
A 670 ASN
A 798 GLN
A 931 ASN
A1148 GLN
A1515 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.110493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.087326 restraints weight = 21608.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.00
r_work: 0.3109 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  14515  Z= 0.216
  Angle     :  0.562  11.648  20172  Z= 0.311
  Chirality :  0.043   0.305   2277
  Planarity :  0.004   0.038   2113
  Dihedral  : 18.102 166.242   3355
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.30 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.23), residues: 1349
  helix:  1.57 (0.20), residues: 637
  sheet: -0.27 (0.38), residues: 164
  loop :  0.56 (0.28), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1078 
 TYR   0.013   0.002   TYR A1265 
 PHE   0.014   0.002   PHE A 540 
 TRP   0.014   0.002   TRP A  87 
 HIS   0.005   0.001   HIS A1177 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00482 /  0.22 (14515)
  covalent geometry    : angle       0.56192 /  0.31 (20172)
  hydrogen bonds       : bond        0.04715 /  3.04 (  659)
  hydrogen bonds       : angle       4.32178 /  3.04 ( 1767)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7510 (tp30)
REVERT: A  418 LYS cc_start: 0.7369 (tppt) cc_final: 0.6961 (ttmm)
REVERT: A  450 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8398 (mp)
REVERT: A  488 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8006 (tm-30)
REVERT: A  515 GLU cc_start: 0.8713 (tt0) cc_final: 0.8220 (tm-30)
REVERT: A  555 GLU cc_start: 0.8490 (tp30) cc_final: 0.8186 (tp30)
REVERT: A  898 GLU cc_start: 0.7952 (tt0) cc_final: 0.7187 (OUTLIER)
REVERT: A  900 ASN cc_start: 0.6257 (OUTLIER) cc_final: 0.6050 (m110)
REVERT: A  938 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7548 (m-40)
REVERT: A  942 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7762 (mm-30)
REVERT: A 1358 MET cc_start: 0.8856 (tpt) cc_final: 0.8431 (tpt)
REVERT: A 1540 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.7886 (mmm160)
REVERT: A 1550 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7943 (ttpp)
REVERT: A 1552 ASP cc_start: 0.9065 (p0) cc_final: 0.8810 (p0)
  outliers start: 26
  outliers final: 12
  residues processed: 114
  average time/residue: 0.5588
  time to fit residues: 70.4685
Evaluate side-chains
  105 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  772 PHE
Chi-restraints excluded: chain A residue  823 HIS
Chi-restraints excluded: chain A residue  855 THR
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  900 ASN
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1550 LYS
Chi-restraints excluded: chain A residue 1622 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 144 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0570
   chunk 5 optimal weight:    0.3980
   chunk 32 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.6498

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 491 GLN
A 604 GLN
A 798 GLN
A 848 GLN
A 931 ASN
A1148 GLN
A1515 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.111954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.088797 restraints weight = 21458.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.00
r_work: 0.3135 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14515  Z= 0.145
  Angle     :  0.519  11.207  20172  Z= 0.293
  Chirality :  0.040   0.300   2277
  Planarity :  0.003   0.038   2113
  Dihedral  : 18.123 167.211   3355
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.71 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.23), residues: 1349
  helix:  1.63 (0.20), residues: 637
  sheet: -0.28 (0.38), residues: 164
  loop :  0.57 (0.28), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1078 
 TYR   0.013   0.001   TYR A1160 
 PHE   0.015   0.001   PHE A1420 
 TRP   0.013   0.001   TRP A  79 
 HIS   0.004   0.001   HIS A1177 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.15 (14515)
  covalent geometry    : angle       0.51912 /  0.29 (20172)
  hydrogen bonds       : bond        0.04299 /  2.75 (  659)
  hydrogen bonds       : angle       4.24438 /  2.98 ( 1767)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7485 (tp30)
REVERT: A  418 LYS cc_start: 0.7358 (tppt) cc_final: 0.6909 (ttmm)
REVERT: A  450 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8356 (mp)
REVERT: A  488 GLN cc_start: 0.8322 (tm-30) cc_final: 0.8049 (tm-30)
REVERT: A  515 GLU cc_start: 0.8714 (tt0) cc_final: 0.8237 (tm-30)
REVERT: A  555 GLU cc_start: 0.8494 (tp30) cc_final: 0.8201 (tp30)
REVERT: A  898 GLU cc_start: 0.7921 (tt0) cc_final: 0.7211 (OUTLIER)
REVERT: A  938 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7471 (m-40)
REVERT: A  942 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7740 (mm-30)
REVERT: A 1038 LYS cc_start: 0.7794 (pttt) cc_final: 0.7579 (ptpt)
REVERT: A 1268 LYS cc_start: 0.8851 (mtmm) cc_final: 0.8573 (mppt)
REVERT: A 1358 MET cc_start: 0.8839 (tpt) cc_final: 0.8414 (tpt)
REVERT: A 1540 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.7910 (mmm160)
REVERT: A 1550 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7930 (ttpp)
REVERT: A 1552 ASP cc_start: 0.9036 (p0) cc_final: 0.8781 (p0)
  outliers start: 21
  outliers final: 12
  residues processed: 109
  average time/residue: 0.4955
  time to fit residues: 60.0349
Evaluate side-chains
  105 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  772 PHE
Chi-restraints excluded: chain A residue  823 HIS
Chi-restraints excluded: chain A residue  855 THR
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  900 ASN
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1550 LYS
Chi-restraints excluded: chain A residue 1622 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 137 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 74 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 41 optimal weight:    0.2980
   chunk 90 optimal weight:    5.9990
   chunk 139 optimal weight:    8.9990
   chunk 123 optimal weight:    0.5980
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  53 ASN
A 491 GLN
A 604 GLN
A 798 GLN
A 931 ASN
A1148 GLN
A1515 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.110854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.087744 restraints weight = 21475.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 1.99
r_work: 0.3116 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14515  Z= 0.188
  Angle     :  0.549  10.976  20172  Z= 0.306
  Chirality :  0.041   0.305   2277
  Planarity :  0.004   0.038   2113
  Dihedral  : 18.126 166.486   3355
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.71 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.23), residues: 1349
  helix:  1.55 (0.20), residues: 639
  sheet: -0.31 (0.38), residues: 164
  loop :  0.52 (0.28), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1078 
 TYR   0.012   0.001   TYR A1265 
 PHE   0.014   0.001   PHE A1420 
 TRP   0.011   0.002   TRP A  79 
 HIS   0.004   0.001   HIS A1177 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.19 (14515)
  covalent geometry    : angle       0.54864 /  0.31 (20172)
  hydrogen bonds       : bond        0.04575 /  2.94 (  659)
  hydrogen bonds       : angle       4.30162 /  3.02 ( 1767)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4476.00 seconds
wall clock time: 77 minutes 19.36 seconds (4639.36 seconds total)