Starting phenix.real_space_refine
on Thu May 15 09:23:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wmh_37652/05_2025/8wmh_37652.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wmh_37652/05_2025/8wmh_37652.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wmh_37652/05_2025/8wmh_37652.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wmh_37652/05_2025/8wmh_37652.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wmh_37652/05_2025/8wmh_37652.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wmh_37652/05_2025/8wmh_37652.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     141      5.49       5
     S      19      5.16       5
     C    7736      2.51       5
     N    2256      2.21       5
     O    2790      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12942
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9980
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1198, 9972
          Classifications: {'peptide': 1198}
          Link IDs: {'PTRANS': 30, 'TRANS': 1167}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 1198, 9972
          Classifications: {'peptide': 1198}
          Link IDs: {'PTRANS': 30, 'TRANS': 1167}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 10172
    Chain: "O"
      Number of atoms: 1900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 1900
          Classifications: {'RNA': 89}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 46, 'rna3p_pyr': 36}
          Link IDs: {'rna2p': 6, 'rna3p': 82}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 532
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 532
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "E"
      Number of atoms: 530
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 530
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AASP A 672 " occ=0.45
      ... (14 atoms not shown)
      pdb=" OD2BASP A 672 " occ=0.55
  Time building chain proxies: 11.87, per 1000 atoms: 0.92
  Number of scatterers: 12942
  At special positions: 0
  Unit cell: (98.5075, 115.828, 137.477, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P     141     15.00
     O    2790      8.00
     N    2256      7.00
     C    7736      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.56
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 15 sheets defined
      44.5% alpha, 11.6% beta
      54 base pairs and 86 stacking pairs defined.
    Time for finding SS restraints: 5.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 27
    Processing helix  chain 'A' and resid 42 through 49
      removed outlier: 3.572A  pdb=" N   LEU A  46 " --> pdb=" O   SER A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 88
    Processing helix  chain 'A' and resid 92 through 98
      removed outlier: 3.764A  pdb=" N   GLN A  98 " --> pdb=" O   HIS A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 144
      removed outlier: 3.518A  pdb=" N   PHE A 133 " --> pdb=" O   PHE A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 152
      No H-bonds generated for 'chain 'A' and resid 150 through 152'
    Processing helix  chain 'A' and resid 153 through 162
      removed outlier: 3.737A  pdb=" N   HIS A 157 " --> pdb=" O   TRP A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 182
    Processing helix  chain 'A' and resid 273 through 288
    Processing helix  chain 'A' and resid 291 through 303
    Processing helix  chain 'A' and resid 317 through 334
      removed outlier: 4.039A  pdb=" N   TYR A 321 " --> pdb=" O   GLU A 317 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLU A 334 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 340
      removed outlier: 6.117A  pdb=" N   GLU A 338 " --> pdb=" O   PHE A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 353
    Processing helix  chain 'A' and resid 356 through 364
    Processing helix  chain 'A' and resid 367 through 373
    Processing helix  chain 'A' and resid 386 through 390
    Processing helix  chain 'A' and resid 419 through 434
    Processing helix  chain 'A' and resid 452 through 465
      removed outlier: 3.542A  pdb=" N   PHE A 456 " --> pdb=" O   THR A 452 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR A 465 " --> pdb=" O   GLU A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 478
    Processing helix  chain 'A' and resid 498 through 511
      removed outlier: 3.638A  pdb=" N   THR A 502 " --> pdb=" O   ASN A 498 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   VAL A 511 " --> pdb=" O   ARG A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 534
    Processing helix  chain 'A' and resid 536 through 551
    Processing helix  chain 'A' and resid 557 through 563
    Processing helix  chain 'A' and resid 576 through 588
      Proline residue:  A 585  - end of helix
    Processing helix  chain 'A' and resid 589 through 593
      removed outlier: 3.718A  pdb=" N   TYR A 592 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 598
    Processing helix  chain 'A' and resid 599 through 612
    Processing helix  chain 'A' and resid 619 through 626
      removed outlier: 3.589A  pdb=" N   ARG A 623 " --> pdb=" O   LYS A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 629
      No H-bonds generated for 'chain 'A' and resid 627 through 629'
    Processing helix  chain 'A' and resid 631 through 635
    Processing helix  chain 'A' and resid 639 through 648
    Processing helix  chain 'A' and resid 662 through 672
      removed outlier: 3.882A  pdb=" N   LEU A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 703
      removed outlier: 3.625A  pdb=" N   GLU A 684 " --> pdb=" O   ASN A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 931 through 935
      removed outlier: 3.623A  pdb=" N   ILE A 934 " --> pdb=" O   THR A 931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 936 through 943
    Processing helix  chain 'A' and resid 965 through 976
      removed outlier: 3.634A  pdb=" N   THR A 969 " --> pdb=" O   ASN A 965 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 977 through 997
      Proline residue:  A 988  - end of helix
    Processing helix  chain 'A' and resid 1017 through 1021
    Processing helix  chain 'A' and resid 1025 through 1030
      removed outlier: 4.105A  pdb=" N   ILE A1029 " --> pdb=" O   LYS A1026 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   ASP A1030 " --> pdb=" O   LYS A1027 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1044
      removed outlier: 4.373A  pdb=" N   ALA A1035 " --> pdb=" O   HIS A1031 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA A1044 " --> pdb=" O   VAL A1040 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1045 through 1054
    Processing helix  chain 'A' and resid 1063 through 1070
    Processing helix  chain 'A' and resid 1101 through 1112
    Processing helix  chain 'A' and resid 1193 through 1198
    Processing helix  chain 'A' and resid 1203 through 1216
    Processing helix  chain 'A' and resid 1219 through 1224
    Processing helix  chain 'A' and resid 1225 through 1235
    Processing helix  chain 'A' and resid 1265 through 1270
      removed outlier: 4.079A  pdb=" N   LYS A1269 " --> pdb=" O   GLY A1266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1299 through 1309
    Processing helix  chain 'A' and resid 1353 through 1358
    Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 715
      removed outlier: 6.589A  pdb=" N   ASN A   4 " --> pdb=" O   GLU A 711 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   HIS A 713 " --> pdb=" O   ASN A   4 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   LEU A   6 " --> pdb=" O   HIS A 713 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   GLU A 715 " --> pdb=" O   LEU A   6 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   LEU A   8 " --> pdb=" O   GLU A 715 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS A   3 " --> pdb=" O   GLN A  22 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ILE A  15 " --> pdb=" O   SER A  36 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   SER A  36 " --> pdb=" O   ILE A  15 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   TRP A  17 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   MET A  34 " --> pdb=" O   TRP A  17 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   LEU A  19 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100
      removed outlier: 3.904A  pdb=" N   LYS A 107 " --> pdb=" O   ASP A 100 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 121
    Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 204
      removed outlier: 3.538A  pdb=" N   LYS A 247 " --> pdb=" O   LEU A 204 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLU A 248 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 211 through 215
      removed outlier: 4.257A  pdb=" N   GLU A 214 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 400
      removed outlier: 4.984A  pdb=" N   LEU A 412 " --> pdb=" O   CYS A 393 " (cutoff:3.500A)
      removed outlier: 9.353A  pdb=" N   LEU A 395 " --> pdb=" O   GLN A 410 " (cutoff:3.500A)
      removed outlier: 10.313A  pdb=" N   GLN A 410 " --> pdb=" O   LEU A 395 " (cutoff:3.500A)
      removed outlier: 10.050A  pdb=" N   PHE A 397 " --> pdb=" O   HIS A 408 " (cutoff:3.500A)
      removed outlier: 10.934A  pdb=" N   HIS A 408 " --> pdb=" O   PHE A 397 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 437 through 438
    Processing sheet with id=AA8, first strand: chain 'A' and resid 468 through 469
      removed outlier: 3.678A  pdb=" N   VAL A 469 " --> pdb=" O   TYR A 495 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   TYR A 495 " --> pdb=" O   VAL A 469 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1071 through 1072
      removed outlier: 4.314A  pdb=" N   GLN A1094 " --> pdb=" O   LYS A1072 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1124 through 1126
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1130 through 1137
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1166 through 1168
      removed outlier: 4.124A  pdb=" N   LEU A1181 " --> pdb=" O   VAL A1168 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1260 through 1261
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1293 through 1298
      removed outlier: 4.661A  pdb=" N   PHE A1282 " --> pdb=" O   ILE A1298 " (cutoff:3.500A)
      removed outlier: 5.740A  pdb=" N   PHE A1283 " --> pdb=" O   ASP A1327 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   ASP A1327 " --> pdb=" O   PHE A1283 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL A1285 " --> pdb=" O   LEU A1325 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1370 through 1375
      removed outlier: 6.897A  pdb=" N   GLU A1370 " --> pdb=" O   THR A1366 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   THR A1366 " --> pdb=" O   GLU A1370 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   TYR A1372 " --> pdb=" O   GLU A1364 " (cutoff:3.500A)

    386 hydrogen bonds defined for protein.
    1077 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      130 hydrogen bonds
      248 hydrogen bond angles
      0 basepair planarities
      54 basepair parallelities
      86 stacking parallelities
  Total time for adding SS restraints: 7.59

  Time building geometry restraints manager: 4.17 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: 2803
        1.33 -     1.45: 3643
        1.45 -     1.57: 6748
        1.57 -     1.69: 278
        1.69 -     1.81: 31
  Bond restraints: 13503
  Sorted by residual:
  bond pdb=" N   GLU A1393 "
       pdb=" CA  GLU A1393 "
    ideal  model  delta    sigma   weight residual
    1.459  1.427  0.033 1.20e-02 6.94e+03 7.34e+00
  bond pdb=" CA  ARG A1122 "
       pdb=" C   ARG A1122 "
    ideal  model  delta    sigma   weight residual
    1.524  1.489  0.035 1.35e-02 5.49e+03 6.71e+00
  bond pdb=" C   ARG A1122 "
       pdb=" N   VAL A1123 "
    ideal  model  delta    sigma   weight residual
    1.333  1.303  0.031 1.46e-02 4.69e+03 4.39e+00
  bond pdb=" CA  ARG A 692 "
       pdb=" CB  ARG A 692 "
    ideal  model  delta    sigma   weight residual
    1.529  1.496  0.032 1.58e-02 4.01e+03 4.22e+00
  bond pdb=" C   GLY A1392 "
       pdb=" N   GLU A1393 "
    ideal  model  delta    sigma   weight residual
    1.334  1.310  0.024 1.33e-02 5.65e+03 3.30e+00
  ... (remaining 13498 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 18331
        1.41 -     2.82: 416
        2.82 -     4.23: 73
        4.23 -     5.64: 18
        5.64 -     7.06: 2
  Bond angle restraints: 18840
  Sorted by residual:
  angle pdb=" N   ARG A 692 "
        pdb=" CA  ARG A 692 "
        pdb=" C   ARG A 692 "
      ideal   model   delta    sigma   weight residual
     111.14  106.19    4.95 1.08e+00 8.57e-01 2.10e+01
  angle pdb=" N   LYS A1417 "
        pdb=" CA  LYS A1417 "
        pdb=" C   LYS A1417 "
      ideal   model   delta    sigma   weight residual
     110.20  115.76   -5.56 1.58e+00 4.01e-01 1.24e+01
  angle pdb=" N   GLU A  72 "
        pdb=" CA  GLU A  72 "
        pdb=" CB  GLU A  72 "
      ideal   model   delta    sigma   weight residual
     110.22  115.13   -4.91 1.54e+00 4.22e-01 1.02e+01
  angle pdb=" N   LYS A 272 "
        pdb=" CA  LYS A 272 "
        pdb=" C   LYS A 272 "
      ideal   model   delta    sigma   weight residual
     114.75  110.93    3.82 1.26e+00 6.30e-01 9.19e+00
  angle pdb=" O3'  DA E  16 "
        pdb=" C3'  DA E  16 "
        pdb=" C2'  DA E  16 "
      ideal   model   delta    sigma   weight residual
     111.50  107.02    4.48 1.50e+00 4.44e-01 8.91e+00
  ... (remaining 18835 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.90: 7223
       24.90 -    49.81: 624
       49.81 -    74.71: 248
       74.71 -    99.62: 19
       99.62 -   124.52: 3
  Dihedral angle restraints: 8117
    sinusoidal: 4590
      harmonic: 3527
  Sorted by residual:
  dihedral pdb=" O4'   C O 113 "
           pdb=" C1'   C O 113 "
           pdb=" N1    C O 113 "
           pdb=" C2    C O 113 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00 -114.43  -45.57     1      1.50e+01 4.44e-03 1.28e+01
  dihedral pdb=" C4'  DA E  17 "
           pdb=" C3'  DA E  17 "
           pdb=" O3'  DA E  17 "
           pdb=" P    DT E  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   95.48  124.52     1      3.50e+01 8.16e-04 1.23e+01
  dihedral pdb=" O4'   G O  94 "
           pdb=" C1'   G O  94 "
           pdb=" N9    G O  94 "
           pdb=" C4    G O  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -156.14   50.14     1      1.70e+01 3.46e-03 1.19e+01
  ... (remaining 8114 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1496
       0.033 -    0.067: 441
       0.067 -    0.100: 116
       0.100 -    0.134: 53
       0.134 -    0.167: 8
  Chirality restraints: 2114
  Sorted by residual:
  chirality pdb=" CA  GLU A  72 "
            pdb=" N   GLU A  72 "
            pdb=" C   GLU A  72 "
            pdb=" CB  GLU A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.99e-01
  chirality pdb=" C3'   G O 107 "
            pdb=" C4'   G O 107 "
            pdb=" O3'   G O 107 "
            pdb=" C2'   G O 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.31   -0.17 2.00e-01 2.50e+01 6.94e-01
  chirality pdb=" CA  LYS A1417 "
            pdb=" N   LYS A1417 "
            pdb=" C   LYS A1417 "
            pdb=" CB  LYS A1417 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.53e-01
  ... (remaining 2111 not shown)

  Planarity restraints: 1895
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  68 "    0.010 2.00e-02 2.50e+03   1.98e-02 3.90e+00
        pdb=" C   ARG A  68 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ARG A  68 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ARG A  69 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 122 "   -0.008 2.00e-02 2.50e+03   1.71e-02 2.94e+00
        pdb=" CG  ASP A 122 "    0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 122 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 122 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 419 "    0.027 5.00e-02 4.00e+02   4.07e-02 2.65e+00
        pdb=" N   PRO A 420 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 420 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 420 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1892 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1058
        2.74 -     3.28: 12693
        3.28 -     3.82: 23035
        3.82 -     4.36: 27866
        4.36 -     4.90: 43888
  Nonbonded interactions: 108540
  Sorted by model distance:
  nonbonded pdb=" O2'   A O 114 "
            pdb=" O4'   A O 115 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   LYS A 109 "
            pdb=" OG1 THR A 112 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OG  SER A 385 "
            pdb=" OP1   C O 118 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OE1 GLU A1132 "
            pdb=" O2'   U O  86 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O2'   G O 107 "
            pdb=" OP1   C O 108 "
     model   vdw
     2.247 3.040
  ... (remaining 108535 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.45 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:             2.170
  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:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     44.380
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:11.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6035
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13503  Z= 0.161
  Angle     :  0.541   7.056  18840  Z= 0.311
  Chirality :  0.038   0.167   2114
  Planarity :  0.003   0.041   1895
  Dihedral  : 19.417 124.521   5835
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.82 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.24), residues: 1195
  helix:  0.98 (0.24), residues: 462
  sheet: -0.59 (0.45), residues: 131
  loop : -0.61 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 528 
 HIS   0.003   0.001   HIS A1033 
 PHE   0.017   0.001   PHE A 990 
 TYR   0.012   0.001   TYR A1380 
 ARG   0.010   0.000   ARG A1028 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15083 (  516)
  hydrogen bonds       : angle       5.84872 ( 1325)
  covalent geometry    : bond        0.00328 (13503)
  covalent geometry    : angle       0.54070 (18840)

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

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 175
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.7347 (tp30) cc_final: 0.6853 (tp30)
REVERT: A   63 LYS cc_start: 0.7101 (tptm) cc_final: 0.6580 (tptm)
REVERT: A   64 TYR cc_start: 0.7694 (m-80) cc_final: 0.7444 (m-80)
REVERT: A   79 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7440 (mt-10)
REVERT: A  103 LYS cc_start: 0.7643 (tptm) cc_final: 0.7363 (tptm)
REVERT: A  129 PHE cc_start: 0.7655 (m-80) cc_final: 0.7207 (m-80)
REVERT: A  265 PHE cc_start: 0.2996 (m-80) cc_final: 0.2680 (m-80)
REVERT: A  280 LYS cc_start: 0.7240 (ttpt) cc_final: 0.6965 (ttmt)
REVERT: A  317 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6240 (mm-30)
REVERT: A  357 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6766 (mm-30)
REVERT: A  373 MET cc_start: 0.8028 (ttp) cc_final: 0.7767 (ttp)
REVERT: A  381 ARG cc_start: 0.7245 (mtt90) cc_final: 0.6955 (mpt180)
REVERT: A  656 MET cc_start: -0.1031 (pmm) cc_final: -0.1284 (pmm)
REVERT: A  980 ASP cc_start: 0.6436 (t0) cc_final: 0.6123 (t0)
REVERT: A 1124 ILE cc_start: 0.7378 (pt) cc_final: 0.7087 (pp)
REVERT: A 1144 GLU cc_start: 0.7477 (pt0) cc_final: 0.7183 (pt0)
REVERT: A 1155 ILE cc_start: 0.7670 (mm) cc_final: 0.7458 (mt)
REVERT: A 1177 LYS cc_start: 0.7579 (ttpt) cc_final: 0.7379 (ttpp)
REVERT: A 1184 THR cc_start: 0.7753 (t) cc_final: 0.7523 (t)
REVERT: A 1186 LYS cc_start: 0.7340 (mmtm) cc_final: 0.7005 (mmtm)
REVERT: A 1238 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7251 (mptt)
REVERT: A 1241 ASP cc_start: 0.7256 (m-30) cc_final: 0.7006 (m-30)
REVERT: A 1243 LYS cc_start: 0.7112 (mttp) cc_final: 0.6782 (mtmm)
REVERT: A 1296 GLU cc_start: 0.7617 (tt0) cc_final: 0.7021 (pt0)
REVERT: A 1311 LEU cc_start: 0.7272 (mt) cc_final: 0.7026 (mt)
REVERT: A 1323 ARG cc_start: 0.6117 (ptt90) cc_final: 0.5809 (ptt90)
  outliers start: 4
  outliers final: 2
  residues processed: 179
  average time/residue: 1.3128
  time to fit residues: 254.6371
Evaluate side-chains
  155 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue 1417 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 110 optimal weight:    0.7980
   chunk 99 optimal weight:    0.1980
   chunk 55 optimal weight:   50.0000
   chunk 33 optimal weight:    0.7980
   chunk 66 optimal weight:    0.3980
   chunk 53 optimal weight:    9.9990
   chunk 102 optimal weight:    1.9990
   chunk 39 optimal weight:   30.0000
   chunk 62 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 118 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 287 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4735 r_free = 0.4735 target = 0.232674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.176006 restraints weight = 40955.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.4060 rms_B_bonded: 3.85
r_work: 0.3842 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3835
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3835 r_free = 0.3835    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3835 r_free = 0.3835    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3835
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13503  Z= 0.178
  Angle     :  0.587  13.765  18840  Z= 0.314
  Chirality :  0.041   0.200   2114
  Planarity :  0.004   0.051   1895
  Dihedral  : 20.823 122.396   3245
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  8.26 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.24), residues: 1195
  helix:  0.91 (0.23), residues: 472
  sheet: -0.47 (0.46), residues: 119
  loop : -0.62 (0.25), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 487 
 HIS   0.004   0.001   HIS A 477 
 PHE   0.013   0.002   PHE A1102 
 TYR   0.014   0.001   TYR A1131 
 ARG   0.009   0.001   ARG A 692 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04637 (  516)
  hydrogen bonds       : angle       4.27421 ( 1325)
  covalent geometry    : bond        0.00390 (13503)
  covalent geometry    : angle       0.58709 (18840)

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

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 167
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.4839 (mmm) cc_final: 0.4632 (mmm)
REVERT: A   69 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.8036 (ttm170)
REVERT: A  168 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7904 (mp0)
REVERT: A  201 PHE cc_start: 0.7489 (t80) cc_final: 0.7175 (t80)
REVERT: A  265 PHE cc_start: 0.3744 (m-80) cc_final: 0.3116 (m-80)
REVERT: A  280 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7753 (ttmm)
REVERT: A  311 LYS cc_start: 0.7956 (tppt) cc_final: 0.7746 (tppp)
REVERT: A  317 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6904 (mm-30)
REVERT: A  350 ARG cc_start: 0.6927 (ttp-110) cc_final: 0.6570 (mtm-85)
REVERT: A  367 ASP cc_start: 0.7486 (p0) cc_final: 0.7282 (p0)
  outliers start: 11
  outliers final: 4
  residues processed: 172
  average time/residue: 1.4343
  time to fit residues: 266.7707
Evaluate side-chains
  150 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 145
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 GLU
Chi-restraints excluded: chain A residue  958 SER
Chi-restraints excluded: chain A residue 1167 LYS
Chi-restraints excluded: chain A residue 1180 ILE
Chi-restraints excluded: chain A residue 1322 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 54 optimal weight:    9.9990
   chunk 66 optimal weight:    0.4980
   chunk 38 optimal weight:    0.0770
   chunk 68 optimal weight:    0.9990
   chunk 85 optimal weight:   20.0000
   chunk 107 optimal weight:    0.7980
   chunk 40 optimal weight:   20.0000
   chunk 91 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.6742

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 283 GLN
A 360 GLN
A 960 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.230369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.181513 restraints weight = 34292.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.4160 rms_B_bonded: 4.94
r_work (final): 0.4160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4159
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4159 r_free = 0.4159    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4159 r_free = 0.4159    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4159
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6648
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13503  Z= 0.185
  Angle     :  0.583  13.394  18840  Z= 0.313
  Chirality :  0.040   0.196   2114
  Planarity :  0.004   0.053   1895
  Dihedral  : 20.770 121.750   3239
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 11.16 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.24), residues: 1195
  helix:  0.76 (0.24), residues: 470
  sheet: -0.47 (0.45), residues: 117
  loop : -0.62 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 528 
 HIS   0.003   0.001   HIS A 359 
 PHE   0.021   0.002   PHE A1024 
 TYR   0.014   0.002   TYR A 937 
 ARG   0.010   0.001   ARG A 381 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04474 (  516)
  hydrogen bonds       : angle       4.16229 ( 1325)
  covalent geometry    : bond        0.00405 (13503)
  covalent geometry    : angle       0.58317 (18840)

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

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 177
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 PHE cc_start: 0.7337 (t80) cc_final: 0.6956 (t80)
REVERT: A  265 PHE cc_start: 0.4069 (m-80) cc_final: 0.3476 (m-80)
REVERT: A  280 LYS cc_start: 0.7756 (ttpt) cc_final: 0.7529 (ttmm)
REVERT: A  317 GLU cc_start: 0.6570 (mm-30) cc_final: 0.6344 (mm-30)
REVERT: A  350 ARG cc_start: 0.6113 (ttp-110) cc_final: 0.5765 (mtm-85)
  outliers start: 26
  outliers final: 8
  residues processed: 188
  average time/residue: 1.3409
  time to fit residues: 272.6771
Evaluate side-chains
  165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 157
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  364 ARG
Chi-restraints excluded: chain A residue  945 ILE
Chi-restraints excluded: chain A residue  958 SER
Chi-restraints excluded: chain A residue 1043 CYS
Chi-restraints excluded: chain A residue 1167 LYS
Chi-restraints excluded: chain A residue 1180 ILE
Chi-restraints excluded: chain A residue 1187 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9990
   chunk 55 optimal weight:   30.0000
   chunk 39 optimal weight:   30.0000
   chunk 35 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 178 ASN
A 283 GLN
A1108 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4686 r_free = 0.4686 target = 0.228132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.168036 restraints weight = 40056.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 3.87
r_work: 0.3762 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3753
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3753 r_free = 0.3753    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3753 r_free = 0.3753    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3753
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  13503  Z= 0.236
  Angle     :  0.627  13.551  18840  Z= 0.336
  Chirality :  0.043   0.196   2114
  Planarity :  0.004   0.054   1895
  Dihedral  : 20.815 119.869   3239
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 13.70 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.24), residues: 1195
  helix:  0.50 (0.23), residues: 472
  sheet: -0.58 (0.43), residues: 125
  loop : -0.66 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 660 
 HIS   0.004   0.001   HIS A1034 
 PHE   0.017   0.002   PHE A1326 
 TYR   0.021   0.002   TYR A1134 
 ARG   0.009   0.001   ARG A1323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04752 (  516)
  hydrogen bonds       : angle       4.24112 ( 1325)
  covalent geometry    : bond        0.00524 (13503)
  covalent geometry    : angle       0.62689 (18840)

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

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 163
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 ARG cc_start: 0.8384 (ttm-80) cc_final: 0.8124 (ttm170)
REVERT: A  201 PHE cc_start: 0.7606 (t80) cc_final: 0.7195 (t80)
REVERT: A  265 PHE cc_start: 0.3856 (m-80) cc_final: 0.2807 (m-80)
REVERT: A  280 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7835 (ttmt)
REVERT: A  317 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6854 (mm-30)
REVERT: A  350 ARG cc_start: 0.6726 (ttp-110) cc_final: 0.6478 (mtm-85)
REVERT: A 1027 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7793 (tptp)
  outliers start: 31
  outliers final: 15
  residues processed: 182
  average time/residue: 1.3485
  time to fit residues: 265.1369
Evaluate side-chains
  172 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  958 SER
Chi-restraints excluded: chain A residue  981 VAL
Chi-restraints excluded: chain A residue 1027 LYS
Chi-restraints excluded: chain A residue 1028 ARG
Chi-restraints excluded: chain A residue 1043 CYS
Chi-restraints excluded: chain A residue 1180 ILE
Chi-restraints excluded: chain A residue 1187 SER
Chi-restraints excluded: chain A residue 1236 ILE
Chi-restraints excluded: chain A residue 1316 LEU
Chi-restraints excluded: chain A residue 1322 SER
Chi-restraints excluded: chain A residue 1366 THR
Chi-restraints excluded: chain A residue 1391 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 34 optimal weight:    0.6980
   chunk 118 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 117 optimal weight:    0.0870
   chunk 37 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 125 optimal weight:   20.0000
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 283 GLN
A1346 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.229075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.181328 restraints weight = 38971.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.4144 rms_B_bonded: 5.35
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4146
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4146 r_free = 0.4146    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4146 r_free = 0.4146    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4146
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6653
moved from start:          0.3931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13503  Z= 0.161
  Angle     :  0.557  13.333  18840  Z= 0.300
  Chirality :  0.040   0.195   2114
  Planarity :  0.004   0.054   1895
  Dihedral  : 20.757 119.833   3239
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.25 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.24), residues: 1195
  helix:  0.68 (0.24), residues: 472
  sheet: -0.86 (0.41), residues: 142
  loop : -0.56 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 528 
 HIS   0.003   0.001   HIS A1034 
 PHE   0.015   0.001   PHE A 990 
 TYR   0.014   0.001   TYR A1134 
 ARG   0.003   0.000   ARG A1323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03949 (  516)
  hydrogen bonds       : angle       4.07908 ( 1325)
  covalent geometry    : bond        0.00352 (13503)
  covalent geometry    : angle       0.55677 (18840)

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

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 PHE cc_start: 0.7364 (t80) cc_final: 0.7028 (t80)
REVERT: A  280 LYS cc_start: 0.7807 (ttpt) cc_final: 0.7552 (ttmt)
REVERT: A  317 GLU cc_start: 0.6554 (mm-30) cc_final: 0.6302 (mm-30)
REVERT: A  350 ARG cc_start: 0.6225 (ttp-110) cc_final: 0.5958 (mtm-85)
  outliers start: 20
  outliers final: 11
  residues processed: 169
  average time/residue: 1.4219
  time to fit residues: 259.9126
Evaluate side-chains
  164 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  958 SER
Chi-restraints excluded: chain A residue  981 VAL
Chi-restraints excluded: chain A residue 1180 ILE
Chi-restraints excluded: chain A residue 1187 SER
Chi-restraints excluded: chain A residue 1236 ILE
Chi-restraints excluded: chain A residue 1316 LEU
Chi-restraints excluded: chain A residue 1322 SER
Chi-restraints excluded: chain A residue 1366 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 104 optimal weight:    0.5980
   chunk 124 optimal weight:    1.9990
   chunk 84 optimal weight:   30.0000
   chunk 73 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 39 optimal weight:   40.0000
   chunk 61 optimal weight:    0.8980
   chunk 78 optimal weight:    0.6980
   chunk 42 optimal weight:    7.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 283 GLN
A 685 GLN
A 710 ASN
A1033 HIS
A1108 HIS
** A1401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.228130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.178244 restraints weight = 37086.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.4120 rms_B_bonded: 4.70
r_work (final): 0.4120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4121
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4121 r_free = 0.4121    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4121 r_free = 0.4121    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4121
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.4220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13503  Z= 0.182
  Angle     :  0.565  13.154  18840  Z= 0.306
  Chirality :  0.040   0.194   2114
  Planarity :  0.004   0.054   1895
  Dihedral  : 20.750 118.881   3239
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.70 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.24), residues: 1195
  helix:  0.62 (0.24), residues: 474
  sheet: -0.65 (0.45), residues: 128
  loop : -0.58 (0.26), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 528 
 HIS   0.007   0.001   HIS A1034 
 PHE   0.016   0.001   PHE A 990 
 TYR   0.017   0.002   TYR A1134 
 ARG   0.004   0.000   ARG A1323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04184 (  516)
  hydrogen bonds       : angle       4.13541 ( 1325)
  covalent geometry    : bond        0.00403 (13503)
  covalent geometry    : angle       0.56543 (18840)

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

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 PHE cc_start: 0.7361 (t80) cc_final: 0.7006 (t80)
REVERT: A  280 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7482 (ttmt)
REVERT: A  350 ARG cc_start: 0.6235 (ttp-110) cc_final: 0.5985 (mtm-85)
REVERT: A 1132 GLU cc_start: 0.6988 (mp0) cc_final: 0.6497 (mp0)
  outliers start: 24
  outliers final: 14
  residues processed: 164
  average time/residue: 1.4059
  time to fit residues: 249.5915
Evaluate side-chains
  162 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  981 VAL
Chi-restraints excluded: chain A residue 1043 CYS
Chi-restraints excluded: chain A residue 1180 ILE
Chi-restraints excluded: chain A residue 1187 SER
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1236 ILE
Chi-restraints excluded: chain A residue 1311 LEU
Chi-restraints excluded: chain A residue 1316 LEU
Chi-restraints excluded: chain A residue 1322 SER
Chi-restraints excluded: chain A residue 1366 THR
Chi-restraints excluded: chain A residue 1391 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 126 optimal weight:   10.0000
   chunk 118 optimal weight:    0.5980
   chunk 2 optimal weight:    0.4980
   chunk 1 optimal weight:    0.8980
   chunk 83 optimal weight:    6.9990
   chunk 116 optimal weight:    0.5980
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 120 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 178 ASN
A 283 GLN
A1108 HIS
A1301 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.228703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.180064 restraints weight = 27887.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.4158 rms_B_bonded: 3.22
r_work: 0.3807 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3793
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3793 r_free = 0.3793    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3793 r_free = 0.3793    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3793
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.4451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13503  Z= 0.165
  Angle     :  0.557  12.036  18840  Z= 0.300
  Chirality :  0.040   0.192   2114
  Planarity :  0.004   0.054   1895
  Dihedral  : 20.617 118.374   3239
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 16.61 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.24), residues: 1195
  helix:  0.75 (0.24), residues: 472
  sheet: -0.96 (0.47), residues: 118
  loop : -0.52 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 528 
 HIS   0.006   0.001   HIS A1033 
 PHE   0.037   0.001   PHE A 669 
 TYR   0.015   0.001   TYR A1239 
 ARG   0.004   0.000   ARG A1323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03948 (  516)
  hydrogen bonds       : angle       4.05802 ( 1325)
  covalent geometry    : bond        0.00365 (13503)
  covalent geometry    : angle       0.55731 (18840)

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

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 1.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.6269 (m-10)
REVERT: A  280 LYS cc_start: 0.8075 (ttpt) cc_final: 0.7792 (ttmt)
REVERT: A  350 ARG cc_start: 0.6731 (ttp-110) cc_final: 0.6457 (mtm-85)
REVERT: A  669 PHE cc_start: 0.7871 (t80) cc_final: 0.7611 (t80)
REVERT: A 1132 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7281 (mp0)
  outliers start: 19
  outliers final: 12
  residues processed: 159
  average time/residue: 1.4179
  time to fit residues: 243.6131
Evaluate side-chains
  160 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 SER
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  232 TYR
Chi-restraints excluded: chain A residue  980 ASP
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1043 CYS
Chi-restraints excluded: chain A residue 1132 GLU
Chi-restraints excluded: chain A residue 1180 ILE
Chi-restraints excluded: chain A residue 1236 ILE
Chi-restraints excluded: chain A residue 1311 LEU
Chi-restraints excluded: chain A residue 1316 LEU
Chi-restraints excluded: chain A residue 1322 SER
Chi-restraints excluded: chain A residue 1366 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 37 optimal weight:    0.3980
   chunk 52 optimal weight:    9.9990
   chunk 81 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 178 ASN
** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 995 GLN
A1108 HIS
A1301 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.226992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.177703 restraints weight = 32704.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.4118 rms_B_bonded: 4.15
r_work: 0.3708 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3696 r_free = 0.3696    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3696 r_free = 0.3696    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.4763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  13503  Z= 0.209
  Angle     :  0.601  12.720  18840  Z= 0.322
  Chirality :  0.042   0.193   2114
  Planarity :  0.004   0.055   1895
  Dihedral  : 20.662 117.564   3239
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 16.88 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.24), residues: 1195
  helix:  0.63 (0.24), residues: 470
  sheet: -0.65 (0.45), residues: 130
  loop : -0.61 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 528 
 HIS   0.005   0.001   HIS A1033 
 PHE   0.031   0.002   PHE A 669 
 TYR   0.021   0.002   TYR A1134 
 ARG   0.006   0.001   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04501 (  516)
  hydrogen bonds       : angle       4.19095 ( 1325)
  covalent geometry    : bond        0.00464 (13503)
  covalent geometry    : angle       0.60056 (18840)

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

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 PHE cc_start: 0.7615 (t80) cc_final: 0.7078 (t80)
REVERT: A  232 TYR cc_start: 0.6718 (OUTLIER) cc_final: 0.6212 (m-10)
REVERT: A  280 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7857 (ttmt)
REVERT: A  350 ARG cc_start: 0.6871 (ttp-110) cc_final: 0.6595 (mtm-85)
REVERT: A  669 PHE cc_start: 0.7923 (t80) cc_final: 0.7660 (t80)
  outliers start: 19
  outliers final: 10
  residues processed: 160
  average time/residue: 1.4453
  time to fit residues: 249.9846
Evaluate side-chains
  156 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  232 TYR
Chi-restraints excluded: chain A residue  980 ASP
Chi-restraints excluded: chain A residue 1043 CYS
Chi-restraints excluded: chain A residue 1180 ILE
Chi-restraints excluded: chain A residue 1236 ILE
Chi-restraints excluded: chain A residue 1311 LEU
Chi-restraints excluded: chain A residue 1322 SER
Chi-restraints excluded: chain A residue 1366 THR
Chi-restraints excluded: chain A residue 1391 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 114 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0170
   chunk 23 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0020
   chunk 42 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.5626

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 283 GLN
A1108 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.228093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.179288 restraints weight = 32431.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.4149 rms_B_bonded: 3.82
r_work: 0.3768 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3753
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3753 r_free = 0.3753    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3753 r_free = 0.3753    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3753
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.4894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13503  Z= 0.163
  Angle     :  0.578  12.237  18840  Z= 0.306
  Chirality :  0.040   0.191   2114
  Planarity :  0.004   0.054   1895
  Dihedral  : 20.609 117.030   3239
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 17.97 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.24), residues: 1195
  helix:  0.69 (0.24), residues: 472
  sheet: -0.75 (0.47), residues: 120
  loop : -0.63 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 528 
 HIS   0.005   0.001   HIS A1033 
 PHE   0.028   0.001   PHE A 669 
 TYR   0.018   0.001   TYR A1134 
 ARG   0.006   0.000   ARG A1323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03939 (  516)
  hydrogen bonds       : angle       4.06117 ( 1325)
  covalent geometry    : bond        0.00360 (13503)
  covalent geometry    : angle       0.57786 (18840)

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

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 151
  time to evaluate  : 1.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7103 (mp0)
REVERT: A  232 TYR cc_start: 0.6680 (OUTLIER) cc_final: 0.6408 (m-10)
REVERT: A  280 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7828 (ttmt)
REVERT: A  350 ARG cc_start: 0.6787 (ttp-110) cc_final: 0.6515 (mtm-85)
REVERT: A  669 PHE cc_start: 0.7869 (t80) cc_final: 0.7633 (t80)
  outliers start: 14
  outliers final: 9
  residues processed: 155
  average time/residue: 1.4211
  time to fit residues: 238.0300
Evaluate side-chains
  156 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  232 TYR
Chi-restraints excluded: chain A residue  980 ASP
Chi-restraints excluded: chain A residue 1043 CYS
Chi-restraints excluded: chain A residue 1236 ILE
Chi-restraints excluded: chain A residue 1311 LEU
Chi-restraints excluded: chain A residue 1322 SER
Chi-restraints excluded: chain A residue 1366 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 48 optimal weight:   10.0000
   chunk 46 optimal weight:    0.0970
   chunk 37 optimal weight:    0.6980
   chunk 125 optimal weight:   30.0000
   chunk 54 optimal weight:   10.0000
   chunk 35 optimal weight:    0.0020
   chunk 123 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 119 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0980
   overall best weight:    0.3386

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 283 GLN
A1108 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.229160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.170647 restraints weight = 42615.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 3.62
r_work: 0.3801 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3793
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3793 r_free = 0.3793    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3793 r_free = 0.3793    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3793
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.4956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13503  Z= 0.131
  Angle     :  0.548  11.888  18840  Z= 0.295
  Chirality :  0.039   0.190   2114
  Planarity :  0.003   0.054   1895
  Dihedral  : 20.550 116.505   3239
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 18.24 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.24), residues: 1195
  helix:  0.74 (0.24), residues: 473
  sheet: -0.62 (0.49), residues: 118
  loop : -0.66 (0.25), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 528 
 HIS   0.005   0.001   HIS A1033 
 PHE   0.026   0.001   PHE A 669 
 TYR   0.016   0.001   TYR A1239 
 ARG   0.005   0.000   ARG A1323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03757 (  516)
  hydrogen bonds       : angle       3.97974 ( 1325)
  covalent geometry    : bond        0.00287 (13503)
  covalent geometry    : angle       0.54795 (18840)

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

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 1.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.7294 (tp30) cc_final: 0.7046 (tp30)
REVERT: A  232 TYR cc_start: 0.6602 (OUTLIER) cc_final: 0.6284 (m-10)
REVERT: A  280 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7767 (ttmt)
REVERT: A  350 ARG cc_start: 0.6762 (ttp-110) cc_final: 0.6497 (mtm-85)
REVERT: A  669 PHE cc_start: 0.7804 (t80) cc_final: 0.7599 (t80)
  outliers start: 13
  outliers final: 8
  residues processed: 156
  average time/residue: 1.4493
  time to fit residues: 244.2435
Evaluate side-chains
  157 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 148
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  232 TYR
Chi-restraints excluded: chain A residue  980 ASP
Chi-restraints excluded: chain A residue 1043 CYS
Chi-restraints excluded: chain A residue 1236 ILE
Chi-restraints excluded: chain A residue 1316 LEU
Chi-restraints excluded: chain A residue 1366 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 76 optimal weight:    0.0670
   chunk 35 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0040
   chunk 88 optimal weight:    0.3980
   chunk 121 optimal weight:    1.9990
   chunk 79 optimal weight:    0.2980
   chunk 48 optimal weight:    0.7980
   chunk 125 optimal weight:   20.0000
   overall best weight:    0.2730

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

Flipped N/Q/H residues before XYZ refinement:
A1108 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.229738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.180305 restraints weight = 24469.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.4160 rms_B_bonded: 2.98
r_work: 0.3844 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3835
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3835 r_free = 0.3835    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3835 r_free = 0.3835    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3835
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.5050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13503  Z= 0.123
  Angle     :  0.546  12.302  18840  Z= 0.293
  Chirality :  0.038   0.188   2114
  Planarity :  0.004   0.059   1895
  Dihedral  : 20.510 115.974   3239
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 18.42 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.24), residues: 1195
  helix:  0.75 (0.24), residues: 473
  sheet: -0.79 (0.45), residues: 132
  loop : -0.63 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 528 
 HIS   0.006   0.001   HIS A1033 
 PHE   0.026   0.001   PHE A 669 
 TYR   0.015   0.001   TYR A1239 
 ARG   0.013   0.000   ARG A1028 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03620 (  516)
  hydrogen bonds       : angle       3.91679 ( 1325)
  covalent geometry    : bond        0.00268 (13503)
  covalent geometry    : angle       0.54597 (18840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11607.93 seconds
wall clock time: 199 minutes 45.17 seconds (11985.17 seconds total)