Starting phenix.real_space_refine
on Wed Mar  4 01:04:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n9w_49179/03_2026/9n9w_49179.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n9w_49179/03_2026/9n9w_49179.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n9w_49179/03_2026/9n9w_49179.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n9w_49179/03_2026/9n9w_49179.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n9w_49179/03_2026/9n9w_49179.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n9w_49179/03_2026/9n9w_49179.map"
  }
  resolution = 3.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.040
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      3      5.21       5
     S      49      5.16       5
     C    5966      2.51       5
     N    1719      2.21       5
     O    1744      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9486
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9370
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1278, 9329
          Classifications: {'peptide': 1278}
          Incomplete info: {'truncation_to_alanine': 124}
          Link IDs: {'PCIS': 1, 'PTRANS': 97, 'TRANS': 1179}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 444
          Unresolved non-hydrogen angles: 556
          Unresolved non-hydrogen dihedrals: 345
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'GLU:plan': 38, 'ASP:plan': 24, 'ARG:plan': 9, 'HIS:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 320
      Conformer: "B"
        Number of residues, atoms: 1278, 9329
          Classifications: {'peptide': 1278}
          Incomplete info: {'truncation_to_alanine': 124}
          Link IDs: {'PCIS': 1, 'PTRANS': 97, 'TRANS': 1179}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 444
          Unresolved non-hydrogen angles: 556
          Unresolved non-hydrogen dihedrals: 345
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'GLU:plan': 38, 'ASP:plan': 24, 'ARG:plan': 9, 'HIS:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 320
          bond proxies already assigned to first conformer: 9521
    Chain: "A"
      Number of atoms: 116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 116
          Unusual residues: {' MG': 3, 'ADP': 1, 'ANP': 1}
          Classifications: {'undetermined': 5, 'water': 55}
          Link IDs: {None: 59}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AARG A  75 " occ=0.24
      ... (20 atoms not shown)
      pdb=" NH2BARG A  75 " occ=0.76
    residue:
      pdb=" N  AARG A 848 " occ=0.55
      ... (20 atoms not shown)
      pdb=" NH2BARG A 848 " occ=0.45
    residue:
      pdb=" N  ALEU A 868 " occ=0.76
      ... (14 atoms not shown)
      pdb=" CD2BLEU A 868 " occ=0.24
    residue:
      pdb=" N  AARG A1310 " occ=0.52
      ... (20 atoms not shown)
      pdb=" NH2BARG A1310 " occ=0.48
  Time building chain proxies: 3.80, per 1000 atoms: 0.40
  Number of scatterers: 9486
  At special positions: 0
  Unit cell: (89.976, 99.104, 101.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      49     16.00
     P       5     15.00
     Mg      3     11.99
     O    1744      8.00
     N    1719      7.00
     C    5966      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 851.1 milliseconds
  

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2320

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 14 sheets defined
      33.4% alpha, 14.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 30
    Processing helix  chain 'A' and resid 53 through 65
      removed outlier: 3.701A  pdb=" N   LEU A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 111
    Processing helix  chain 'A' and resid 134 through 146
      removed outlier: 3.804A  pdb=" N   HIS A 146 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 191
      removed outlier: 4.607A  pdb=" N   LEU A 184 " --> pdb=" O   GLY A 180 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   GLU A 185 " --> pdb=" O   ARG A 181 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   LYS A 186 " --> pdb=" O   LEU A 182 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ALA A 187 " --> pdb=" O   ALA A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 211
      removed outlier: 5.242A  pdb=" N   LYS A 205 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLN A 208 " --> pdb=" O   THR A 204 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   GLU A 209 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LEU A 210 " --> pdb=" O   ARG A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 226
      removed outlier: 3.723A  pdb=" N   ASN A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 256
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 318 through 336
    Processing helix  chain 'A' and resid 377 through 397
      removed outlier: 4.163A  pdb=" N   SER A 386 " --> pdb=" O   ALA A 382 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASN A 387 " --> pdb=" O   ILE A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 504
    Processing helix  chain 'A' and resid 520 through 530
      removed outlier: 4.048A  pdb=" N   ASN A 524 " --> pdb=" O   GLY A 520 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A 525 " --> pdb=" O   GLY A 521 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLU A 528 " --> pdb=" O   ASN A 524 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   SER A 530 " --> pdb=" O   LEU A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 556
    Processing helix  chain 'A' and resid 571 through 579
    Processing helix  chain 'A' and resid 629 through 633
    Processing helix  chain 'A' and resid 660 through 669
      removed outlier: 4.205A  pdb=" N   ARG A 667 " --> pdb=" O   GLN A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 682
    Processing helix  chain 'A' and resid 728 through 732
    Processing helix  chain 'A' and resid 735 through 752
    Processing helix  chain 'A' and resid 776 through 796
      removed outlier: 3.878A  pdb=" N   ALA A 780 " --> pdb=" O   GLY A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 871
      removed outlier: 3.534A  pdb=" N   GLN A 870 " --> pdb=" O   THR A 866 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 901
      removed outlier: 3.543A  pdb=" N   LEU A 888 " --> pdb=" O   LEU A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 914 through 925
    Processing helix  chain 'A' and resid 941 through 946
    Processing helix  chain 'A' and resid 960 through 971
      removed outlier: 3.870A  pdb=" N   ALA A 971 " --> pdb=" O   ARG A 967 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1003 through 1012
      removed outlier: 4.060A  pdb=" N   LEU A1007 " --> pdb=" O   PRO A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1024 through 1038
    Processing helix  chain 'A' and resid 1075 through 1087
    Processing helix  chain 'A' and resid 1094 through 1101
      removed outlier: 3.568A  pdb=" N   LEU A1098 " --> pdb=" O   THR A1094 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1117 through 1121
    Processing helix  chain 'A' and resid 1126 through 1135
    Processing helix  chain 'A' and resid 1136 through 1148
    Processing helix  chain 'A' and resid 1158 through 1167
    Processing helix  chain 'A' and resid 1242 through 1252
    Processing helix  chain 'A' and resid 1297 through 1301
    Processing helix  chain 'A' and resid 1311 through 1316
      removed outlier: 3.997A  pdb=" N   THR A1316 " --> pdb=" O   PRO A1312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1322 through 1334
      removed outlier: 4.090A  pdb=" N   PHE A1326 " --> pdb=" O   TRP A1322 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8
      removed outlier: 3.557A  pdb=" N   GLY A  35 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ARG A 118 " --> pdb=" O   ASN A  45 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 245
    Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 286
      removed outlier: 5.487A  pdb=" N   ALA A 275 " --> pdb=" O   PHE A 306 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   PHE A 306 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   GLN A 277 " --> pdb=" O   VAL A 304 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   VAL A 304 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LYS A 279 " --> pdb=" O   ARG A 302 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ARG A 302 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL A 281 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLY A 300 " --> pdb=" O   VAL A 281 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ARG A 285 " --> pdb=" O   GLN A 296 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   SER A 293 " --> pdb=" O   ASP A1092 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   VAL A1090 " --> pdb=" O   PHE A 295 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   VAL A1065 " --> pdb=" O   TRP A1091 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 310
      removed outlier: 3.645A  pdb=" N   ALA A 345 " --> pdb=" O   ILE A 430 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   SER A 432 " --> pdb=" O   VAL A 343 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   VAL A 343 " --> pdb=" O   SER A 432 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 411
      removed outlier: 3.860A  pdb=" N   LEU A 410 " --> pdb=" O   ARG A 418 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 511 through 516
      removed outlier: 4.850A  pdb=" N   SER A 513 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 590 through 591
    Processing sheet with id=AA8, first strand: chain 'A' and resid 692 through 694
      removed outlier: 6.071A  pdb=" N   VAL A 710 " --> pdb=" O   ALA A 693 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 767 through 768
    Processing sheet with id=AB1, first strand: chain 'A' and resid 810 through 812
    Processing sheet with id=AB2, first strand: chain 'A' and resid 956 through 957
      removed outlier: 6.910A  pdb=" N   GLY A 849 " --> pdb=" O   HIS A 980 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   HIS A 980 " --> pdb=" O   GLY A 849 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   LEU A 851 " --> pdb=" O   LEU A 978 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 851 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   TYR A 853 " --> pdb=" O   LEU A 976 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   HIS A 974 " --> pdb=" O   ALA A 855 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 930 through 934
      removed outlier: 5.842A  pdb=" N   LEU A 930 " --> pdb=" O   ARG A 991 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   SER A 993 " --> pdb=" O   LEU A 930 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   VAL A 932 " --> pdb=" O   SER A 993 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   VAL A 994 " --> pdb=" O   VAL A 998 " (cutoff:3.500A)
      removed outlier: 5.559A  pdb=" N   VAL A 998 " --> pdb=" O   VAL A 994 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1192 through 1195
      removed outlier: 3.525A  pdb=" N   ALA A1239 " --> pdb=" O   LEU A1193 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1226 through 1233

    347 hydrogen bonds defined for protein.
    978 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.74

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1531
        1.27 -     1.41: 2389
        1.41 -     1.54: 5639
        1.54 -     1.68: 42
        1.68 -     1.81: 72
  Bond restraints: 9673
  Sorted by residual:
  bond pdb=" O3A ANP A1402 "
       pdb=" PB  ANP A1402 "
    ideal  model  delta    sigma   weight residual
    1.700  1.557  0.143 2.00e-02 2.50e+03 5.09e+01
  bond pdb=" C   ASP A 901 "
       pdb=" O   ASP A 901 "
    ideal  model  delta    sigma   weight residual
    1.232  1.138  0.094 1.35e-02 5.49e+03 4.83e+01
  bond pdb=" CA  ASP A 901 "
       pdb=" C   ASP A 901 "
    ideal  model  delta    sigma   weight residual
    1.527  1.463  0.063 1.19e-02 7.06e+03 2.84e+01
  bond pdb=" N3B ANP A1402 "
       pdb=" PG  ANP A1402 "
    ideal  model  delta    sigma   weight residual
    1.795  1.693  0.102 2.00e-02 2.50e+03 2.58e+01
  bond pdb=" C   GLU A 983 "
       pdb=" O   GLU A 983 "
    ideal  model  delta    sigma   weight residual
    1.235  1.173  0.062 1.26e-02 6.30e+03 2.45e+01
  ... (remaining 9668 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.25: 13093
        3.25 -     6.49: 122
        6.49 -     9.74: 13
        9.74 -    12.98: 1
       12.98 -    16.23: 1
  Bond angle restraints: 13230
  Sorted by residual:
  angle pdb=" N   ILE A 357 "
        pdb=" CA  ILE A 357 "
        pdb=" C   ILE A 357 "
      ideal   model   delta    sigma   weight residual
     108.95  100.59    8.36 9.80e-01 1.04e+00 7.28e+01
  angle pdb=" N   VAL A 939 "
        pdb=" CA  VAL A 939 "
        pdb=" C   VAL A 939 "
      ideal   model   delta    sigma   weight residual
     109.20   99.79    9.41 1.55e+00 4.16e-01 3.69e+01
  angle pdb=" CA  GLY A 982 "
        pdb=" C   GLY A 982 "
        pdb=" O   GLY A 982 "
      ideal   model   delta    sigma   weight residual
     121.60  115.82    5.78 9.70e-01 1.06e+00 3.56e+01
  angle pdb=" PB  ANP A1402 "
        pdb=" N3B ANP A1402 "
        pdb=" PG  ANP A1402 "
      ideal   model   delta    sigma   weight residual
     126.95  110.72   16.23 3.00e+00 1.11e-01 2.93e+01
  angle pdb=" CA  ASP A 901 "
        pdb=" C   ASP A 901 "
        pdb=" N   ARG A 902 "
      ideal   model   delta    sigma   weight residual
     115.68  121.87   -6.19 1.24e+00 6.50e-01 2.49e+01
  ... (remaining 13225 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.47: 5341
       28.47 -    56.94: 371
       56.94 -    85.41: 30
       85.41 -   113.88: 2
      113.88 -   142.35: 1
  Dihedral angle restraints: 5745
    sinusoidal: 2125
      harmonic: 3620
  Sorted by residual:
  dihedral pdb=" CA  SER A 579 "
           pdb=" C   SER A 579 "
           pdb=" N   ALA A 580 "
           pdb=" CA  ALA A 580 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.32   22.68     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" O1A ANP A1402 "
           pdb=" O3A ANP A1402 "
           pdb=" PA  ANP A1402 "
           pdb=" PB  ANP A1402 "
      ideal   model   delta sinusoidal    sigma   weight residual
      83.11  -59.24  142.35     1      3.00e+01 1.11e-03 1.91e+01
  dihedral pdb=" CA  ASP A 201 "
           pdb=" C   ASP A 201 "
           pdb=" N   PHE A 202 "
           pdb=" CA  PHE A 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.40   21.60     0      5.00e+00 4.00e-02 1.87e+01
  ... (remaining 5742 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1261
       0.056 -    0.111: 185
       0.111 -    0.167: 30
       0.167 -    0.222: 3
       0.222 -    0.278: 4
  Chirality restraints: 1483
  Sorted by residual:
  chirality pdb=" CA  VAL A 941 "
            pdb=" N   VAL A 941 "
            pdb=" C   VAL A 941 "
            pdb=" CB  VAL A 941 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.16    0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  ILE A 357 "
            pdb=" N   ILE A 357 "
            pdb=" C   ILE A 357 "
            pdb=" CB  ILE A 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" C3' ANP A1402 "
            pdb=" C2' ANP A1402 "
            pdb=" C4' ANP A1402 "
            pdb=" O3' ANP A1402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.62    0.26 2.00e-01 2.50e+01 1.75e+00
  ... (remaining 1480 not shown)

  Planarity restraints: 1744
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 546 "   -0.044 5.00e-02 4.00e+02   6.68e-02 7.15e+00
        pdb=" N   PRO A 547 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 547 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 547 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 900 "   -0.012 2.00e-02 2.50e+03   2.29e-02 5.24e+00
        pdb=" C   LYS A 900 "    0.040 2.00e-02 2.50e+03
        pdb=" O   LYS A 900 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASP A 901 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 934 "    0.037 5.00e-02 4.00e+02   5.58e-02 4.97e+00
        pdb=" N   PRO A 935 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 935 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 935 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1741 not shown)

  Histogram of nonbonded interaction distances:
        1.79 -     2.41: 48
        2.41 -     3.03: 6102
        3.03 -     3.66: 14239
        3.66 -     4.28: 21891
        4.28 -     4.90: 38173
  Nonbonded interactions: 80453
  Sorted by model distance:
  nonbonded pdb=" O2B ADP A1401 "
            pdb="MG    MG A1405 "
     model   vdw
     1.791 2.170
  nonbonded pdb=" O3B ADP A1401 "
            pdb="MG    MG A1404 "
     model   vdw
     1.859 2.170
  nonbonded pdb=" OD2 ASP A 909 "
            pdb="MG    MG A1405 "
     model   vdw
     1.873 2.170
  nonbonded pdb=" OD1 ASP A 909 "
            pdb="MG    MG A1405 "
     model   vdw
     1.919 2.170
  nonbonded pdb=" OD2 ASP A 912 "
            pdb="MG    MG A1403 "
     model   vdw
     1.946 2.170
  ... (remaining 80448 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.24 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:             2.040
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     12.710
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6652
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.143   9673  Z= 0.278
  Angle     :  0.755  16.231  13230  Z= 0.400
  Chirality :  0.045   0.278   1483
  Planarity :  0.006   0.067   1744
  Dihedral  : 17.717 142.351   3425
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  9.00 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 27.10 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.98 (0.24), residues: 1278
  helix:  0.35 (0.27), residues: 394
  sheet: -2.05 (0.41), residues: 171
  loop : -2.17 (0.23), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1303 
 TYR   0.028   0.002   TYR A1202 
 PHE   0.015   0.001   PHE A 269 
 TRP   0.006   0.001   TRP A 555 
 HIS   0.005   0.001   HIS A 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 9673)
  covalent geometry    : angle       0.75535 (13230)
  hydrogen bonds       : bond        0.18210 (  347)
  hydrogen bonds       : angle       8.20326 (  978)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 212
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  273 SER cc_start: 0.7245 (OUTLIER) cc_final: 0.6377 (m)
REVERT: A  288 ASP cc_start: 0.6911 (t0) cc_final: 0.6646 (m-30)
REVERT: A  337 THR cc_start: 0.7564 (t) cc_final: 0.6870 (t)
REVERT: A  394 ASN cc_start: 0.5000 (m-40) cc_final: 0.4725 (m-40)
REVERT: A  438 ILE cc_start: 0.7782 (mm) cc_final: 0.7512 (mm)
REVERT: A  447 MET cc_start: 0.5294 (mtm) cc_final: 0.4974 (mtt)
REVERT: A  507 LYS cc_start: 0.8270 (mppt) cc_final: 0.7800 (mppt)
REVERT: A  717 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6646 (mm-30)
REVERT: A  808 MET cc_start: 0.6475 (tpp) cc_final: 0.5955 (tpp)
REVERT: A  835 THR cc_start: 0.8335 (p) cc_final: 0.7901 (t)
REVERT: A  968 TYR cc_start: 0.6957 (m-80) cc_final: 0.6420 (m-80)
REVERT: A 1136 HIS cc_start: 0.7505 (t-90) cc_final: 0.7237 (t70)
  outliers start: 4
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1020
  time to fit residues: 30.4092
Evaluate side-chains
  170 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 169
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 123 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0050
   chunk 51 optimal weight:    0.4980
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 524 ASN
A 543 GLN
A 896 GLN
A 908 HIS
A1074 ASN
A1159 ASN
** A1233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.123191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.109542 restraints weight = 49368.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 4.08
r_work: 0.3272 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3278
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   9673  Z= 0.193
  Angle     :  0.758  10.334  13230  Z= 0.378
  Chirality :  0.048   0.216   1483
  Planarity :  0.007   0.064   1744
  Dihedral  :  7.185 129.332   1422
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.66 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 27.65 %
    Favored  : 69.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.24), residues: 1278
  helix:  0.36 (0.26), residues: 392
  sheet: -2.32 (0.35), residues: 227
  loop : -1.94 (0.24), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1109 
 TYR   0.019   0.002   TYR A1202 
 PHE   0.019   0.002   PHE A 924 
 TRP   0.018   0.002   TRP A 555 
 HIS   0.011   0.001   HIS A 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 9673)
  covalent geometry    : angle       0.75778 (13230)
  hydrogen bonds       : bond        0.03637 (  347)
  hydrogen bonds       : angle       5.86638 (  978)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 177
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 LEU cc_start: 0.7752 (mt) cc_final: 0.7372 (mp)
REVERT: A  288 ASP cc_start: 0.7162 (t0) cc_final: 0.6795 (m-30)
REVERT: A  302 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7728 (mtt180)
REVERT: A  312 ASN cc_start: 0.7788 (m-40) cc_final: 0.7508 (m-40)
REVERT: A  337 THR cc_start: 0.7807 (t) cc_final: 0.7523 (t)
REVERT: A  394 ASN cc_start: 0.5051 (m-40) cc_final: 0.4679 (m-40)
REVERT: A  434 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7084 (mp0)
REVERT: A  438 ILE cc_start: 0.7944 (mm) cc_final: 0.7728 (mm)
REVERT: A  507 LYS cc_start: 0.8561 (mppt) cc_final: 0.8256 (mppt)
REVERT: A  649 MET cc_start: 0.7074 (tmm) cc_final: 0.6797 (tmm)
REVERT: A  757 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7491 (m)
REVERT: A  803 LYS cc_start: 0.7772 (mttp) cc_final: 0.7418 (mttp)
REVERT: A  968 TYR cc_start: 0.7821 (m-80) cc_final: 0.6899 (m-80)
REVERT: A 1039 MET cc_start: 0.6590 (mtp) cc_final: 0.6309 (mmm)
REVERT: A 1103 ILE cc_start: 0.8476 (tp) cc_final: 0.8193 (pt)
REVERT: A 1162 GLN cc_start: 0.7390 (mt0) cc_final: 0.7020 (mt0)
REVERT: A 1202 TYR cc_start: 0.8031 (t80) cc_final: 0.7581 (t80)
REVERT: A 1248 GLN cc_start: 0.7115 (tt0) cc_final: 0.6819 (tm-30)
  outliers start: 26
  outliers final: 13
  residues processed: 198
  average time/residue: 0.0910
  time to fit residues: 26.0635
Evaluate side-chains
  176 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 162
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  757 THR
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue 1125 SER
Chi-restraints excluded: chain A residue 1158 CYS
Chi-restraints excluded: chain A residue 1159 ASN
Chi-restraints excluded: chain A residue 1277 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 35 optimal weight:    0.2980
   chunk 7 optimal weight:    1.9990
   chunk 96 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 99 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 272 ASN
A 524 ASN
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 878 HIS
A 908 HIS
A1074 ASN
** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1233 HIS
** A1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.121200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.106791 restraints weight = 45896.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 4.41
r_work: 0.3238 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.3360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9673  Z= 0.171
  Angle     :  0.705  11.781  13230  Z= 0.346
  Chirality :  0.046   0.191   1483
  Planarity :  0.006   0.062   1744
  Dihedral  :  7.143 132.236   1421
  Min Nonbonded Distance : 1.848

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  6.79 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 28.31 %
    Favored  : 68.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.74 (0.24), residues: 1278
  helix:  0.42 (0.26), residues: 395
  sheet: -2.03 (0.36), residues: 214
  loop : -1.85 (0.24), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 583 
 TYR   0.018   0.002   TYR A 679 
 PHE   0.021   0.002   PHE A  64 
 TRP   0.023   0.002   TRP A1206 
 HIS   0.008   0.001   HIS A1258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 9673)
  covalent geometry    : angle       0.70471 (13230)
  hydrogen bonds       : bond        0.03696 (  347)
  hydrogen bonds       : angle       5.45135 (  978)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 198
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A   27 GLN cc_start: 0.8058 (tp40) cc_final: 0.7811 (tp40)
REVERT: A  174 ILE cc_start: 0.5895 (OUTLIER) cc_final: 0.5348 (mt)
REVERT: A  283 PHE cc_start: 0.7107 (p90) cc_final: 0.6811 (p90)
REVERT: A  288 ASP cc_start: 0.7254 (t0) cc_final: 0.6898 (m-30)
REVERT: A  337 THR cc_start: 0.8059 (t) cc_final: 0.7767 (t)
REVERT: A  491 MET cc_start: 0.7963 (tpp) cc_final: 0.7671 (tpp)
REVERT: A  507 LYS cc_start: 0.8723 (mppt) cc_final: 0.8333 (mppt)
REVERT: A  649 MET cc_start: 0.7037 (tmm) cc_final: 0.6821 (tmm)
REVERT: A  803 LYS cc_start: 0.8100 (mttp) cc_final: 0.7671 (mttp)
REVERT: A  830 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8484 (t)
REVERT: A 1162 GLN cc_start: 0.7682 (mt0) cc_final: 0.7136 (mt0)
REVERT: A 1202 TYR cc_start: 0.8097 (t80) cc_final: 0.7847 (t80)
REVERT: A 1248 GLN cc_start: 0.7159 (tt0) cc_final: 0.6732 (tm-30)
  outliers start: 21
  outliers final: 13
  residues processed: 212
  average time/residue: 0.0902
  time to fit residues: 27.4331
Evaluate side-chains
  202 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 187
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  495 MET
Chi-restraints excluded: chain A residue  524 ASN
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  830 VAL
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue 1013 GLU
Chi-restraints excluded: chain A residue 1074 ASN
Chi-restraints excluded: chain A residue 1238 VAL
Chi-restraints excluded: chain A residue 1294 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 118 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 120 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 17 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 87 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 524 ASN
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 908 HIS
A1074 ASN
** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1159 ASN
** A1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.120957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.106039 restraints weight = 52200.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 4.82
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3418
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3418
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.4206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   9673  Z= 0.171
  Angle     :  0.695  10.448  13230  Z= 0.343
  Chirality :  0.045   0.166   1483
  Planarity :  0.006   0.061   1744
  Dihedral  :  7.030 127.445   1421
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.58 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 27.87 %
    Favored  : 68.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.24), residues: 1278
  helix:  0.44 (0.27), residues: 394
  sheet: -2.22 (0.35), residues: 217
  loop : -1.74 (0.24), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  24 
 TYR   0.012   0.002   TYR A 679 
 PHE   0.012   0.002   PHE A 426 
 TRP   0.020   0.002   TRP A1309 
 HIS   0.009   0.001   HIS A 662 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 9673)
  covalent geometry    : angle       0.69502 (13230)
  hydrogen bonds       : bond        0.03465 (  347)
  hydrogen bonds       : angle       5.28782 (  978)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 201
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A   27 GLN cc_start: 0.7827 (tp40) cc_final: 0.7574 (tp40)
REVERT: A  105 VAL cc_start: 0.7637 (p) cc_final: 0.7435 (m)
REVERT: A  145 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7738 (mp)
REVERT: A  174 ILE cc_start: 0.5977 (OUTLIER) cc_final: 0.5420 (mt)
REVERT: A  337 THR cc_start: 0.8113 (t) cc_final: 0.7845 (t)
REVERT: A  491 MET cc_start: 0.7695 (tpp) cc_final: 0.7380 (tpp)
REVERT: A  507 LYS cc_start: 0.8656 (mppt) cc_final: 0.8142 (mppt)
REVERT: A  524 ASN cc_start: 0.7436 (OUTLIER) cc_final: 0.7091 (t0)
REVERT: A  681 THR cc_start: 0.8087 (p) cc_final: 0.7688 (m)
REVERT: A  803 LYS cc_start: 0.7802 (mttp) cc_final: 0.7266 (mttp)
REVERT: A  812 VAL cc_start: 0.7708 (t) cc_final: 0.7176 (m)
REVERT: A  830 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8252 (t)
REVERT: A 1039 MET cc_start: 0.6674 (mmm) cc_final: 0.6304 (mmm)
REVERT: A 1095 MET cc_start: 0.6744 (mmm) cc_final: 0.6528 (mmm)
REVERT: A 1202 TYR cc_start: 0.7990 (t80) cc_final: 0.7749 (t80)
  outliers start: 30
  outliers final: 13
  residues processed: 221
  average time/residue: 0.0879
  time to fit residues: 27.9717
Evaluate side-chains
  207 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 190
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  495 MET
Chi-restraints excluded: chain A residue  524 ASN
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  757 THR
Chi-restraints excluded: chain A residue  830 VAL
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue 1013 GLU
Chi-restraints excluded: chain A residue 1016 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0980
   chunk 107 optimal weight:    0.3980
   chunk 1 optimal weight:    0.8980
   chunk 114 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 64 optimal weight:    0.2980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 387 ASN
A 493 GLN
A 524 ASN
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 861 HIS
A 908 HIS
A1074 ASN
A1096 GLN
A1136 HIS
A1159 ASN
A1233 HIS
** A1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.123375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.109610 restraints weight = 40384.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 4.07
r_work: 0.3285 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3285
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9673  Z= 0.136
  Angle     :  0.661  10.708  13230  Z= 0.322
  Chirality :  0.044   0.160   1483
  Planarity :  0.006   0.058   1744
  Dihedral  :  6.948 124.806   1421
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.50 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 27.65 %
    Favored  : 68.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.24), residues: 1278
  helix:  0.58 (0.27), residues: 393
  sheet: -1.88 (0.36), residues: 197
  loop : -1.78 (0.23), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 583 
 TYR   0.010   0.001   TYR A 679 
 PHE   0.017   0.001   PHE A1153 
 TRP   0.020   0.001   TRP A1206 
 HIS   0.008   0.001   HIS A1233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9673)
  covalent geometry    : angle       0.66114 (13230)
  hydrogen bonds       : bond        0.03195 (  347)
  hydrogen bonds       : angle       5.06999 (  978)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 198
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A   27 GLN cc_start: 0.7987 (tp40) cc_final: 0.7779 (tp40)
REVERT: A  105 VAL cc_start: 0.7903 (p) cc_final: 0.7675 (m)
REVERT: A  145 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7887 (mp)
REVERT: A  174 ILE cc_start: 0.6346 (OUTLIER) cc_final: 0.5907 (mt)
REVERT: A  337 THR cc_start: 0.8141 (t) cc_final: 0.7916 (t)
REVERT: A  434 GLU cc_start: 0.7917 (mp0) cc_final: 0.7608 (mp0)
REVERT: A  491 MET cc_start: 0.7960 (tpp) cc_final: 0.7699 (tpp)
REVERT: A  507 LYS cc_start: 0.8781 (mppt) cc_final: 0.8249 (mppt)
REVERT: A  649 MET cc_start: 0.6825 (tmm) cc_final: 0.6507 (tmm)
REVERT: A  708 VAL cc_start: 0.8190 (p) cc_final: 0.7981 (p)
REVERT: A  803 LYS cc_start: 0.8181 (mttp) cc_final: 0.7690 (mttp)
REVERT: A  808 MET cc_start: 0.7937 (tpp) cc_final: 0.7219 (tpp)
REVERT: A  812 VAL cc_start: 0.7762 (t) cc_final: 0.7225 (m)
REVERT: A  830 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8454 (t)
REVERT: A 1039 MET cc_start: 0.7016 (mmm) cc_final: 0.6768 (mmm)
REVERT: A 1103 ILE cc_start: 0.8635 (tp) cc_final: 0.8161 (pt)
  outliers start: 30
  outliers final: 16
  residues processed: 219
  average time/residue: 0.0870
  time to fit residues: 27.7479
Evaluate side-chains
  210 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 191
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  757 THR
Chi-restraints excluded: chain A residue  830 VAL
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue 1013 GLU
Chi-restraints excluded: chain A residue 1016 PHE
Chi-restraints excluded: chain A residue 1074 ASN
Chi-restraints excluded: chain A residue 1195 ARG
Chi-restraints excluded: chain A residue 1238 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 87 optimal weight:    0.3980
   chunk 82 optimal weight:    4.9990
   chunk 71 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 48 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 116 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 335 GLN
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 524 ASN
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 861 HIS
A 908 HIS
A1074 ASN
A1136 HIS
A1159 ASN
** A1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.121755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.107137 restraints weight = 48694.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 4.69
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3432
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3432
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.5034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   9673  Z= 0.162
  Angle     :  0.677   9.606  13230  Z= 0.332
  Chirality :  0.045   0.148   1483
  Planarity :  0.006   0.057   1744
  Dihedral  :  7.027 124.715   1421
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  6.95 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 27.76 %
    Favored  : 68.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.24), residues: 1278
  helix:  0.60 (0.27), residues: 395
  sheet: -2.07 (0.35), residues: 209
  loop : -1.71 (0.24), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1300 
 TYR   0.011   0.002   TYR A1119 
 PHE   0.024   0.002   PHE A1153 
 TRP   0.017   0.002   TRP A1309 
 HIS   0.005   0.001   HIS A 908 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 9673)
  covalent geometry    : angle       0.67669 (13230)
  hydrogen bonds       : bond        0.03294 (  347)
  hydrogen bonds       : angle       5.02385 (  978)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 192
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  105 VAL cc_start: 0.7717 (p) cc_final: 0.7452 (m)
REVERT: A  113 LEU cc_start: 0.8202 (mt) cc_final: 0.7915 (mp)
REVERT: A  145 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7860 (mp)
REVERT: A  174 ILE cc_start: 0.6279 (OUTLIER) cc_final: 0.5624 (mt)
REVERT: A  271 ASP cc_start: 0.6807 (t70) cc_final: 0.6565 (t70)
REVERT: A  302 ARG cc_start: 0.7951 (mtt-85) cc_final: 0.7743 (mtt90)
REVERT: A  337 THR cc_start: 0.8263 (t) cc_final: 0.8023 (t)
REVERT: A  416 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7114 (mm110)
REVERT: A  434 GLU cc_start: 0.7506 (mp0) cc_final: 0.7229 (mp0)
REVERT: A  491 MET cc_start: 0.7618 (tpp) cc_final: 0.7269 (tpp)
REVERT: A  507 LYS cc_start: 0.8670 (mppt) cc_final: 0.8146 (mppt)
REVERT: A  588 PHE cc_start: 0.7733 (m-80) cc_final: 0.7514 (m-80)
REVERT: A  649 MET cc_start: 0.6216 (tmm) cc_final: 0.5793 (tmm)
REVERT: A  803 LYS cc_start: 0.7772 (mttp) cc_final: 0.7383 (mttp)
REVERT: A  808 MET cc_start: 0.7818 (tpp) cc_final: 0.7164 (tpp)
REVERT: A  812 VAL cc_start: 0.7788 (t) cc_final: 0.7368 (m)
REVERT: A  830 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8108 (t)
REVERT: A 1039 MET cc_start: 0.6845 (mmm) cc_final: 0.6615 (mmm)
REVERT: A 1103 ILE cc_start: 0.8530 (tp) cc_final: 0.8071 (pt)
REVERT: A 1231 SER cc_start: 0.8519 (m) cc_final: 0.8189 (p)
REVERT: A 1323 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7229 (tt)
  outliers start: 30
  outliers final: 15
  residues processed: 214
  average time/residue: 0.0911
  time to fit residues: 27.8910
Evaluate side-chains
  206 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 187
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  830 VAL
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1013 GLU
Chi-restraints excluded: chain A residue 1016 PHE
Chi-restraints excluded: chain A residue 1195 ARG
Chi-restraints excluded: chain A residue 1238 VAL
Chi-restraints excluded: chain A residue 1323 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0970
   chunk 84 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 123 optimal weight:    0.6980
   chunk 108 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 68 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN
** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 662 HIS
** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 861 HIS
A1074 ASN
A1159 ASN
** A1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.122956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.109049 restraints weight = 42554.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 4.24
r_work: 0.3267 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3266
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3266
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.5377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9673  Z= 0.148
  Angle     :  0.665   9.954  13230  Z= 0.323
  Chirality :  0.044   0.140   1483
  Planarity :  0.006   0.056   1744
  Dihedral  :  6.921 123.606   1421
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.50 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 28.63 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.23), residues: 1278
  helix:  0.48 (0.26), residues: 404
  sheet: -1.88 (0.36), residues: 195
  loop : -1.83 (0.23), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1300 
 TYR   0.014   0.002   TYR A1119 
 PHE   0.031   0.001   PHE A1153 
 TRP   0.035   0.002   TRP A1206 
 HIS   0.005   0.001   HIS A 662 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9673)
  covalent geometry    : angle       0.66501 (13230)
  hydrogen bonds       : bond        0.03223 (  347)
  hydrogen bonds       : angle       4.96611 (  978)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 193
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  105 VAL cc_start: 0.7969 (p) cc_final: 0.7696 (m)
REVERT: A  113 LEU cc_start: 0.8413 (mt) cc_final: 0.8160 (mp)
REVERT: A  145 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7965 (mp)
REVERT: A  174 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.5844 (mt)
REVERT: A  288 ASP cc_start: 0.7494 (t0) cc_final: 0.7199 (t0)
REVERT: A  302 ARG cc_start: 0.8223 (mtt-85) cc_final: 0.8008 (mtt180)
REVERT: A  416 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7456 (mm110)
REVERT: A  434 GLU cc_start: 0.7946 (mp0) cc_final: 0.7698 (mp0)
REVERT: A  491 MET cc_start: 0.7937 (tpp) cc_final: 0.7593 (tpp)
REVERT: A  507 LYS cc_start: 0.8868 (mppt) cc_final: 0.8349 (mppt)
REVERT: A  649 MET cc_start: 0.6768 (tmm) cc_final: 0.6308 (tmm)
REVERT: A  812 VAL cc_start: 0.7774 (t) cc_final: 0.7301 (m)
REVERT: A  830 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8365 (t)
REVERT: A 1205 ARG cc_start: 0.8187 (tpt170) cc_final: 0.7972 (mmt180)
REVERT: A 1231 SER cc_start: 0.8708 (m) cc_final: 0.8433 (p)
REVERT: A 1323 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7431 (tt)
  outliers start: 26
  outliers final: 15
  residues processed: 211
  average time/residue: 0.0824
  time to fit residues: 24.7003
Evaluate side-chains
  205 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 186
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  830 VAL
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1013 GLU
Chi-restraints excluded: chain A residue 1016 PHE
Chi-restraints excluded: chain A residue 1074 ASN
Chi-restraints excluded: chain A residue 1125 SER
Chi-restraints excluded: chain A residue 1195 ARG
Chi-restraints excluded: chain A residue 1323 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 116 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 41 optimal weight:    0.2980
   chunk 107 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 122 optimal weight:    0.5980
   chunk 111 optimal weight:    0.6980
   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 226 ASN
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 861 HIS
A 874 GLN
A 908 HIS
A1074 ASN
** A1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1258 HIS ** 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 = 0.3628 r_free = 0.3628 target = 0.123059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.108924 restraints weight = 46089.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 4.45
r_work: 0.3257 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3262
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3262
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.5575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9673  Z= 0.144
  Angle     :  0.660  10.931  13230  Z= 0.320
  Chirality :  0.044   0.165   1483
  Planarity :  0.006   0.055   1744
  Dihedral  :  6.864 122.613   1421
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.42 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 29.40 %
    Favored  : 67.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.24), residues: 1278
  helix:  0.62 (0.27), residues: 395
  sheet: -1.86 (0.36), residues: 194
  loop : -1.77 (0.23), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 583 
 TYR   0.010   0.002   TYR A  42 
 PHE   0.034   0.001   PHE A1153 
 TRP   0.029   0.002   TRP A1206 
 HIS   0.004   0.001   HIS A 908 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 9673)
  covalent geometry    : angle       0.65971 (13230)
  hydrogen bonds       : bond        0.03195 (  347)
  hydrogen bonds       : angle       4.95272 (  978)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 198
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A  105 VAL cc_start: 0.7974 (p) cc_final: 0.7686 (m)
REVERT: A  113 LEU cc_start: 0.8423 (mt) cc_final: 0.8175 (mp)
REVERT: A  145 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7963 (mp)
REVERT: A  154 PHE cc_start: 0.8516 (m-80) cc_final: 0.8278 (m-10)
REVERT: A  174 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.6021 (mt)
REVERT: A  267 LEU cc_start: 0.8551 (mp) cc_final: 0.8327 (mt)
REVERT: A  416 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7507 (mm110)
REVERT: A  433 MET cc_start: 0.7870 (mtm) cc_final: 0.7608 (mtm)
REVERT: A  434 GLU cc_start: 0.7929 (mp0) cc_final: 0.7624 (mp0)
REVERT: A  491 MET cc_start: 0.7948 (tpp) cc_final: 0.7577 (tpp)
REVERT: A  507 LYS cc_start: 0.8895 (mppt) cc_final: 0.8404 (mppt)
REVERT: A  649 MET cc_start: 0.6857 (tmm) cc_final: 0.6332 (tmm)
REVERT: A  792 MET cc_start: 0.7549 (mmt) cc_final: 0.7348 (mmt)
REVERT: A  812 VAL cc_start: 0.7771 (t) cc_final: 0.7317 (m)
REVERT: A  830 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8295 (t)
REVERT: A 1024 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7358 (mm-30)
REVERT: A 1231 SER cc_start: 0.8686 (m) cc_final: 0.8425 (p)
REVERT: A 1323 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7443 (tt)
  outliers start: 27
  outliers final: 18
  residues processed: 219
  average time/residue: 0.0968
  time to fit residues: 30.1646
Evaluate side-chains
  209 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 187
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  830 VAL
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1013 GLU
Chi-restraints excluded: chain A residue 1074 ASN
Chi-restraints excluded: chain A residue 1125 SER
Chi-restraints excluded: chain A residue 1195 ARG
Chi-restraints excluded: chain A residue 1238 VAL
Chi-restraints excluded: chain A residue 1299 GLU
Chi-restraints excluded: chain A residue 1323 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 123 optimal weight:    0.7980
   chunk 111 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0970
   chunk 93 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 90 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 861 HIS
A1022 GLN
A1074 ASN
** A1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.122609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.107735 restraints weight = 53723.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 4.89
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3430
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3430
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.5758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9673  Z= 0.148
  Angle     :  0.658  12.114  13230  Z= 0.319
  Chirality :  0.044   0.169   1483
  Planarity :  0.006   0.055   1744
  Dihedral  :  6.833 122.431   1421
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.06 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 29.73 %
    Favored  : 67.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.24), residues: 1278
  helix:  0.64 (0.27), residues: 396
  sheet: -1.82 (0.35), residues: 208
  loop : -1.75 (0.24), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 583 
 TYR   0.014   0.002   TYR A1119 
 PHE   0.035   0.002   PHE A1153 
 TRP   0.044   0.002   TRP A1206 
 HIS   0.003   0.001   HIS A 715 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 9673)
  covalent geometry    : angle       0.65850 (13230)
  hydrogen bonds       : bond        0.03198 (  347)
  hydrogen bonds       : angle       4.91386 (  978)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A  105 VAL cc_start: 0.7734 (p) cc_final: 0.7461 (m)
REVERT: A  113 LEU cc_start: 0.8247 (mt) cc_final: 0.7989 (mp)
REVERT: A  145 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7908 (mp)
REVERT: A  174 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.6023 (mt)
REVERT: A  416 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7148 (mm110)
REVERT: A  433 MET cc_start: 0.7333 (mtm) cc_final: 0.7131 (mtm)
REVERT: A  434 GLU cc_start: 0.7498 (mp0) cc_final: 0.7166 (mp0)
REVERT: A  491 MET cc_start: 0.7549 (tpp) cc_final: 0.7133 (tpp)
REVERT: A  507 LYS cc_start: 0.8740 (mppt) cc_final: 0.8279 (mppt)
REVERT: A  649 MET cc_start: 0.6167 (tmm) cc_final: 0.5679 (tmm)
REVERT: A  792 MET cc_start: 0.7307 (mmt) cc_final: 0.7086 (mmt)
REVERT: A  812 VAL cc_start: 0.7756 (t) cc_final: 0.7409 (m)
REVERT: A  830 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8120 (t)
REVERT: A 1231 SER cc_start: 0.8450 (m) cc_final: 0.8181 (p)
REVERT: A 1248 GLN cc_start: 0.7085 (tm-30) cc_final: 0.6267 (tm-30)
  outliers start: 23
  outliers final: 18
  residues processed: 211
  average time/residue: 0.0993
  time to fit residues: 29.3897
Evaluate side-chains
  213 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 192
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  830 VAL
Chi-restraints excluded: chain A residue  838 VAL
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1013 GLU
Chi-restraints excluded: chain A residue 1074 ASN
Chi-restraints excluded: chain A residue 1125 SER
Chi-restraints excluded: chain A residue 1195 ARG
Chi-restraints excluded: chain A residue 1238 VAL
Chi-restraints excluded: chain A residue 1299 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 61 optimal weight:    0.0770
   chunk 58 optimal weight:    0.0060
   chunk 13 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0070
   chunk 80 optimal weight:    0.8980
   chunk 53 optimal weight:    0.1980
   chunk 46 optimal weight:    0.7980
   chunk 115 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0980
   overall best weight:    0.0772

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 238 GLN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 702 GLN
A 861 HIS
A1074 ASN
** A1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1258 HIS ** 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 = 0.3669 r_free = 0.3669 target = 0.126324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.111995 restraints weight = 45616.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 4.50
r_work: 0.3287 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3289
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3289
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.5918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9673  Z= 0.113
  Angle     :  0.647  14.302  13230  Z= 0.312
  Chirality :  0.043   0.162   1483
  Planarity :  0.006   0.061   1744
  Dihedral  :  6.629 116.522   1421
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.87 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 30.05 %
    Favored  : 67.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.24), residues: 1278
  helix:  0.66 (0.27), residues: 405
  sheet: -1.83 (0.35), residues: 211
  loop : -1.73 (0.24), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 458 
 TYR   0.010   0.001   TYR A1119 
 PHE   0.034   0.001   PHE A1153 
 TRP   0.030   0.002   TRP A1206 
 HIS   0.002   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9673)
  covalent geometry    : angle       0.64663 (13230)
  hydrogen bonds       : bond        0.03018 (  347)
  hydrogen bonds       : angle       4.80456 (  978)

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

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

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2556 Ramachandran restraints generated.
    1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 191
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  105 VAL cc_start: 0.7965 (p) cc_final: 0.7667 (m)
REVERT: A  113 LEU cc_start: 0.8393 (mt) cc_final: 0.8156 (mp)
REVERT: A  145 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7789 (mt)
REVERT: A  416 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7425 (mm110)
REVERT: A  433 MET cc_start: 0.7819 (mtm) cc_final: 0.7580 (mtm)
REVERT: A  434 GLU cc_start: 0.7892 (mp0) cc_final: 0.7530 (mp0)
REVERT: A  491 MET cc_start: 0.7933 (tpp) cc_final: 0.7562 (tpp)
REVERT: A  507 LYS cc_start: 0.8876 (mppt) cc_final: 0.8386 (mppt)
REVERT: A  649 MET cc_start: 0.6854 (tmm) cc_final: 0.6294 (tmm)
REVERT: A  792 MET cc_start: 0.7510 (mmt) cc_final: 0.7293 (mmt)
REVERT: A  808 MET cc_start: 0.7874 (tpp) cc_final: 0.7668 (mmt)
REVERT: A  812 VAL cc_start: 0.7726 (t) cc_final: 0.7304 (m)
REVERT: A  830 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8269 (t)
REVERT: A  906 SER cc_start: 0.8148 (p) cc_final: 0.7651 (m)
REVERT: A 1070 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7400 (mm-30)
REVERT: A 1231 SER cc_start: 0.8626 (m) cc_final: 0.8414 (p)
REVERT: A 1323 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7388 (tt)
  outliers start: 21
  outliers final: 15
  residues processed: 205
  average time/residue: 0.0973
  time to fit residues: 28.2091
Evaluate side-chains
  207 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 189
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  830 VAL
Chi-restraints excluded: chain A residue  990 VAL
Chi-restraints excluded: chain A residue 1013 GLU
Chi-restraints excluded: chain A residue 1074 ASN
Chi-restraints excluded: chain A residue 1125 SER
Chi-restraints excluded: chain A residue 1238 VAL
Chi-restraints excluded: chain A residue 1299 GLU
Chi-restraints excluded: chain A residue 1323 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0570
   chunk 3 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 122 optimal weight:    0.0020
   chunk 32 optimal weight:    0.5980
   chunk 97 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0970
   overall best weight:    0.2904

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

Flipped N/Q/H residues before XYZ refinement:
A 248 HIS
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 662 HIS
** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 861 HIS
A 908 HIS
A1074 ASN
A1096 GLN
** A1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.125472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.110193 restraints weight = 47204.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 4.88
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3452
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.5959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9673  Z= 0.117
  Angle     :  0.636  13.369  13230  Z= 0.306
  Chirality :  0.043   0.166   1483
  Planarity :  0.006   0.067   1744
  Dihedral  :  6.553 116.850   1421
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.71 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 30.05 %
    Favored  : 67.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.24), residues: 1278
  helix:  0.84 (0.27), residues: 397
  sheet: -1.69 (0.36), residues: 206
  loop : -1.70 (0.23), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 458 
 TYR   0.011   0.001   TYR A1119 
 PHE   0.034   0.001   PHE A1153 
 TRP   0.028   0.001   TRP A1309 
 HIS   0.007   0.001   HIS A1297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9673)
  covalent geometry    : angle       0.63568 (13230)
  hydrogen bonds       : bond        0.02985 (  347)
  hydrogen bonds       : angle       4.74611 (  978)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2161.15 seconds
wall clock time: 37 minutes 45.10 seconds (2265.10 seconds total)