Starting phenix.real_space_refine
on Wed Apr 30 20:26:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iz9_35836/04_2025/8iz9_35836_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iz9_35836/04_2025/8iz9_35836.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iz9_35836/04_2025/8iz9_35836.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iz9_35836/04_2025/8iz9_35836.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iz9_35836/04_2025/8iz9_35836_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iz9_35836/04_2025/8iz9_35836_trim.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.075
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: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    6351      2.51       5
     N    1638      2.21       5
     O    1747      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9779
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1224, 9754
          Classifications: {'peptide': 1224}
          Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1185}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'XPG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.47, per 1000 atoms: 0.56
  Number of scatterers: 9779
  At special positions: 0
  Unit cell: (74.385, 103.455, 153.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1747      8.00
     N    1638      7.00
     C    6351      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: 2.48
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2312

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 3 sheets defined
      70.0% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 24
    Processing helix  chain 'A' and resid 27 through 37
      removed outlier: 3.575A  pdb=" N   LYS A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 44
      removed outlier: 3.516A  pdb=" N   ASP A  43 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   MET A  44 " --> pdb=" O   GLU A  41 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 40 through 44'
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 74
      removed outlier: 3.622A  pdb=" N   LEU A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ASP A  74 " --> pdb=" O   ARG A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 122
      removed outlier: 5.801A  pdb=" N   LYS A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   SER A  91 " --> pdb=" O   CYS A  87 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   VAL A  94 " --> pdb=" O   LYS A  90 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU A  95 " --> pdb=" O   SER A  91 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   PHE A  98 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
      removed outlier: 3.602A  pdb=" N   TYR A 119 " --> pdb=" O   LYS A 115 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   PHE A 120 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLU A 121 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ASN A 122 " --> pdb=" O   ASN A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 179
      removed outlier: 3.817A  pdb=" N   LEU A 131 " --> pdb=" O   ASP A 127 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   HIS A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 189
    Processing helix  chain 'A' and resid 190 through 213
      removed outlier: 3.501A  pdb=" N   ILE A 194 " --> pdb=" O   THR A 190 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   VAL A 202 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   ASN A 203 " --> pdb=" O   SER A 199 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   PHE A 205 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ASP A 206 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   GLN A 207 " --> pdb=" O   ASN A 203 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   THR A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   VAL A 210 " --> pdb=" O   ASP A 206 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   PHE A 211 " --> pdb=" O   GLN A 207 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   HIS A 213 " --> pdb=" O   THR A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 234
      Proline residue:  A 219  - end of helix
    Processing helix  chain 'A' and resid 236 through 282
      removed outlier: 4.420A  pdb=" N   GLY A 240 " --> pdb=" O   SER A 236 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   LEU A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      Proline residue:  A 249  - end of helix
      removed outlier: 3.769A  pdb=" N   PHE A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLY A 282 " --> pdb=" O   GLU A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 290
      removed outlier: 3.546A  pdb=" N   ILE A 286 " --> pdb=" O   GLY A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 343
      removed outlier: 4.067A  pdb=" N   LYS A 309 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   SER A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   LYS A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLY A 343 " --> pdb=" O   TYR A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 391
      removed outlier: 4.092A  pdb=" N   PHE A 369 " --> pdb=" O   VAL A 365 " (cutoff:3.500A)
      Proline residue:  A 370  - end of helix
    Processing helix  chain 'A' and resid 450 through 459
      removed outlier: 3.683A  pdb=" N   LEU A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 495
    Processing helix  chain 'A' and resid 500 through 510
    Processing helix  chain 'A' and resid 513 through 520
    Processing helix  chain 'A' and resid 522 through 526
      removed outlier: 3.983A  pdb=" N   THR A 526 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 550
    Processing helix  chain 'A' and resid 566 through 578
    Processing helix  chain 'A' and resid 581 through 585
      removed outlier: 4.316A  pdb=" N   GLU A 584 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 597
      removed outlier: 3.524A  pdb=" N   LEU A 597 " --> pdb=" O   LEU A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 622
    Processing helix  chain 'A' and resid 697 through 709
      removed outlier: 4.018A  pdb=" N   TYR A 701 " --> pdb=" O   GLY A 697 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   GLY A 708 " --> pdb=" O   TYR A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 751
      removed outlier: 3.922A  pdb=" N   ASP A 732 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 807
      removed outlier: 3.602A  pdb=" N   TYR A 764 " --> pdb=" O   ASP A 760 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS A 807 " --> pdb=" O   GLU A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 816
      removed outlier: 4.092A  pdb=" N   PHE A 813 " --> pdb=" O   PRO A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 861
      removed outlier: 3.914A  pdb=" N   ASP A 828 " --> pdb=" O   ARG A 824 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ILE A 829 " --> pdb=" O   PHE A 825 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   LEU A 836 " --> pdb=" O   LEU A 832 " (cutoff:3.500A)
      Proline residue:  A 837  - end of helix
    Processing helix  chain 'A' and resid 862 through 866
      removed outlier: 3.894A  pdb=" N   ALA A 865 " --> pdb=" O   PRO A 862 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE A 866 " --> pdb=" O   TRP A 863 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 862 through 866'
    Processing helix  chain 'A' and resid 867 through 910
      removed outlier: 3.940A  pdb=" N   THR A 885 " --> pdb=" O   TYR A 881 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ASP A 888 " --> pdb=" O   GLU A 884 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   SER A 898 " --> pdb=" O   SER A 894 " (cutoff:3.500A)
      Proline residue:  A 899  - end of helix
      removed outlier: 3.547A  pdb=" N   GLY A 910 " --> pdb=" O   SER A 906 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 910 through 918
    Processing helix  chain 'A' and resid 919 through 970
      removed outlier: 4.057A  pdb=" N   CYS A 923 " --> pdb=" O   ALA A 919 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 971 through 974
      removed outlier: 3.797A  pdb=" N   LEU A 974 " --> pdb=" O   ALA A 971 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 971 through 974'
    Processing helix  chain 'A' and resid 975 through 987
    Processing helix  chain 'A' and resid 991 through 1018
      removed outlier: 4.436A  pdb=" N   ILE A1008 " --> pdb=" O   GLU A1004 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   SER A1009 " --> pdb=" O   ASN A1005 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL A1010 " --> pdb=" O   MET A1006 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1090
    Processing helix  chain 'A' and resid 1130 through 1136
    Processing helix  chain 'A' and resid 1142 through 1153
      removed outlier: 4.294A  pdb=" N   LEU A1146 " --> pdb=" O   THR A1142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1155 through 1160
      removed outlier: 3.718A  pdb=" N   ILE A1159 " --> pdb=" O   LEU A1155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1178 through 1193
    Processing helix  chain 'A' and resid 1208 through 1223
    Processing helix  chain 'A' and resid 1258 through 1264
      removed outlier: 3.597A  pdb=" N   ASN A1264 " --> pdb=" O   VAL A1260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1267 through 1276
      removed outlier: 3.893A  pdb=" N   LYS A1271 " --> pdb=" O   SER A1267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1277 through 1297
      removed outlier: 3.513A  pdb=" N   TYR A1297 " --> pdb=" O   PHE A1293 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 475 through 477
      removed outlier: 4.383A  pdb=" N   ALA A 476 " --> pdb=" O   ILE A 555 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   LEU A 557 " --> pdb=" O   ALA A 476 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LEU A 558 " --> pdb=" O   ILE A 588 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL A 590 " --> pdb=" O   LEU A 558 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   LEU A 441 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL A 444 " --> pdb=" O   LEU A 604 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ILE A 603 " --> pdb=" O   GLY A 615 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   GLY A 615 " --> pdb=" O   ILE A 603 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1041 through 1042
      removed outlier: 4.175A  pdb=" N   TRP A1099 " --> pdb=" O   ILE A1042 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1228 through 1232
      removed outlier: 6.486A  pdb=" N   VAL A1071 " --> pdb=" O   THR A1230 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   ALA A1232 " --> pdb=" O   VAL A1071 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ILE A1073 " --> pdb=" O   ALA A1232 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   MET A1245 " --> pdb=" O   GLY A1072 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   VAL A1074 " --> pdb=" O   MET A1245 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   LEU A1247 " --> pdb=" O   VAL A1074 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ASP A1256 " --> pdb=" O   ILE A1244 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   VAL A1246 " --> pdb=" O   GLU A1254 " (cutoff:3.500A)
      removed outlier: 5.392A  pdb=" N   GLU A1254 " --> pdb=" O   VAL A1246 " (cutoff:3.500A)

    608 hydrogen bonds defined for protein.
    1806 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: 3.13

  Time building geometry restraints manager: 2.88 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1616
        1.32 -     1.45: 2596
        1.45 -     1.57: 5705
        1.57 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 9987
  Sorted by residual:
  bond pdb=" C13 XPG A1401 "
       pdb=" C14 XPG A1401 "
    ideal  model  delta    sigma   weight residual
    1.328  1.292  0.036 2.00e-02 2.50e+03 3.30e+00
  bond pdb=" C18 XPG A1401 "
       pdb=" C19 XPG A1401 "
    ideal  model  delta    sigma   weight residual
    1.524  1.497  0.027 2.00e-02 2.50e+03 1.86e+00
  bond pdb=" C2  XPG A1401 "
       pdb=" C3  XPG A1401 "
    ideal  model  delta    sigma   weight residual
    1.520  1.495  0.025 2.00e-02 2.50e+03 1.61e+00
  bond pdb=" N   ASN A1139 "
       pdb=" CA  ASN A1139 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.015 1.29e-02 6.01e+03 1.32e+00
  bond pdb=" C17 XPG A1401 "
       pdb=" C18 XPG A1401 "
    ideal  model  delta    sigma   weight residual
    1.524  1.501  0.023 2.00e-02 2.50e+03 1.28e+00
  ... (remaining 9982 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 13363
        2.03 -     4.07: 137
        4.07 -     6.10: 29
        6.10 -     8.13: 1
        8.13 -    10.17: 3
  Bond angle restraints: 13533
  Sorted by residual:
  angle pdb=" CA  LEU A  13 "
        pdb=" CB  LEU A  13 "
        pdb=" CG  LEU A  13 "
      ideal   model   delta    sigma   weight residual
     116.30  126.47  -10.17 3.50e+00 8.16e-02 8.44e+00
  angle pdb=" C12 XPG A1401 "
        pdb=" C8  XPG A1401 "
        pdb=" C7  XPG A1401 "
      ideal   model   delta    sigma   weight residual
     114.63  123.33   -8.70 3.00e+00 1.11e-01 8.42e+00
  angle pdb=" C7  XPG A1401 "
        pdb=" C8  XPG A1401 "
        pdb=" C9  XPG A1401 "
      ideal   model   delta    sigma   weight residual
     115.09  106.64    8.45 3.00e+00 1.11e-01 7.92e+00
  angle pdb=" N   LYS A1156 "
        pdb=" CA  LYS A1156 "
        pdb=" C   LYS A1156 "
      ideal   model   delta    sigma   weight residual
     111.36  113.96   -2.60 1.09e+00 8.42e-01 5.68e+00
  angle pdb=" N   GLY A1072 "
        pdb=" CA  GLY A1072 "
        pdb=" C   GLY A1072 "
      ideal   model   delta    sigma   weight residual
     111.46  115.55   -4.09 1.75e+00 3.27e-01 5.46e+00
  ... (remaining 13528 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.80: 5420
       18.80 -    37.61: 458
       37.61 -    56.41: 70
       56.41 -    75.21: 19
       75.21 -    94.02: 11
  Dihedral angle restraints: 5978
    sinusoidal: 2407
      harmonic: 3571
  Sorted by residual:
  dihedral pdb=" CA  ASP A1212 "
           pdb=" CB  ASP A1212 "
           pdb=" CG  ASP A1212 "
           pdb=" OD1 ASP A1212 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.05   59.05     1      2.00e+01 2.50e-03 1.17e+01
  dihedral pdb=" C15 XPG A1401 "
           pdb=" C16 XPG A1401 "
           pdb=" C17 XPG A1401 "
           pdb=" C18 XPG A1401 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -176.15  -82.13  -94.02     1      3.00e+01 1.11e-03 1.14e+01
  dihedral pdb=" CB  LYS A1194 "
           pdb=" CG  LYS A1194 "
           pdb=" CD  LYS A1194 "
           pdb=" CE  LYS A1194 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.92  -57.92     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 5975 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1124
       0.036 -    0.072: 352
       0.072 -    0.108: 79
       0.108 -    0.144: 17
       0.144 -    0.180: 1
  Chirality restraints: 1573
  Sorted by residual:
  chirality pdb=" CB  VAL A1153 "
            pdb=" CA  VAL A1153 "
            pdb=" CG1 VAL A1153 "
            pdb=" CG2 VAL A1153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.06e-01
  chirality pdb=" C15 XPG A1401 "
            pdb=" C14 XPG A1401 "
            pdb=" C16 XPG A1401 "
            pdb=" O15 XPG A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.25    2.39   -0.14 2.00e-01 2.50e+01 5.13e-01
  chirality pdb=" CA  ILE A1073 "
            pdb=" N   ILE A1073 "
            pdb=" C   ILE A1073 "
            pdb=" CB  ILE A1073 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.51e-01
  ... (remaining 1570 not shown)

  Planarity restraints: 1682
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C12 XPG A1401 "    0.101 2.00e-02 2.50e+03   2.09e-01 4.36e+02
        pdb=" C13 XPG A1401 "   -0.285 2.00e-02 2.50e+03
        pdb=" C14 XPG A1401 "    0.274 2.00e-02 2.50e+03
        pdb=" C15 XPG A1401 "   -0.090 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  11 "   -0.020 5.00e-02 4.00e+02   3.08e-02 1.51e+00
        pdb=" N   PRO A  12 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A  12 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A  12 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 898 "    0.017 5.00e-02 4.00e+02   2.62e-02 1.10e+00
        pdb=" N   PRO A 899 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 899 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 899 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1679 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2439
        2.80 -     3.32: 9552
        3.32 -     3.85: 16149
        3.85 -     4.37: 17170
        4.37 -     4.90: 30635
  Nonbonded interactions: 75945
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 269 "
            pdb=" OE2 GLU A 306 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" NE2 HIS A 153 "
            pdb=" OD2 ASP A 953 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" O   GLY A 450 "
            pdb=" OG  SER A 453 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   VAL A 484 "
            pdb=" OG  SER A 906 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OH  TYR A 504 "
            pdb=" OD2 ASP A 524 "
     model   vdw
     2.308 3.040
  ... (remaining 75940 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.200
  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:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     23.830
  Find NCS groups from input model:        0.110
  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:12.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5823
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      :  0.002   0.036   9987  Z= 0.126
  Angle     :  0.562  10.169  13533  Z= 0.310
  Chirality :  0.037   0.180   1573
  Planarity :  0.006   0.209   1682
  Dihedral  : 14.569  94.017   3666
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.23), residues: 1218
  helix:  0.38 (0.18), residues: 784
  sheet: -1.45 (0.81), residues: 37
  loop : -2.59 (0.26), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 763 
 HIS   0.003   0.000   HIS A 592 
 PHE   0.006   0.001   PHE A1043 
 TYR   0.017   0.001   TYR A1270 
 ARG   0.001   0.000   ARG A 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10781 (  608)
  hydrogen bonds       : angle       4.24158 ( 1806)
  covalent geometry    : bond        0.00220 ( 9987)
  covalent geometry    : angle       0.56150 (13533)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1145 GLU cc_start: 0.6429 (mp0) cc_final: 0.6208 (pm20)
  outliers start: 0
  outliers final: 2
  residues processed: 137
  average time/residue: 1.3268
  time to fit residues: 194.8409
Evaluate side-chains
  82 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  380 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    7.9990
   chunk 92 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0370
   chunk 31 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   chunk 95 optimal weight:    0.4980
   chunk 37 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 71 optimal weight:    0.6980
   chunk 110 optimal weight:    0.8980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 HIS
A 297 ASN
A 816 ASN
A 931 GLN
** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1275 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4866 r_free = 0.4866 target = 0.266704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.215253 restraints weight = 11753.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.4434 rms_B_bonded: 2.24
r_work: 0.4223 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.4104 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6778
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9987  Z= 0.146
  Angle     :  0.607  12.233  13533  Z= 0.303
  Chirality :  0.042   0.152   1573
  Planarity :  0.004   0.047   1682
  Dihedral  :  4.991  60.283   1355
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.86 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.24), residues: 1218
  helix:  1.51 (0.19), residues: 789
  sheet: -0.76 (0.85), residues: 35
  loop : -1.93 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1025 
 HIS   0.005   0.001   HIS A1111 
 PHE   0.013   0.001   PHE A 352 
 TYR   0.024   0.002   TYR A1255 
 ARG   0.009   0.001   ARG A1012 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04519 (  608)
  hydrogen bonds       : angle       3.52146 ( 1806)
  covalent geometry    : bond        0.00305 ( 9987)
  covalent geometry    : angle       0.60738 (13533)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 ILE cc_start: 0.8000 (mt) cc_final: 0.7782 (mp)
REVERT: A  164 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7380 (ttp)
REVERT: A  186 MET cc_start: 0.5077 (tpt) cc_final: 0.4819 (mmm)
REVERT: A  270 ASP cc_start: 0.6453 (m-30) cc_final: 0.5819 (m-30)
REVERT: A  552 ASP cc_start: 0.7265 (m-30) cc_final: 0.6929 (m-30)
REVERT: A  705 PHE cc_start: 0.8043 (m-10) cc_final: 0.7611 (m-10)
REVERT: A  834 ASP cc_start: 0.6909 (m-30) cc_final: 0.6603 (t70)
REVERT: A  912 TRP cc_start: 0.6032 (m-10) cc_final: 0.5523 (m-90)
REVERT: A 1002 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7284 (mp0)
REVERT: A 1015 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7510 (tt0)
REVERT: A 1047 ASN cc_start: 0.3704 (m-40) cc_final: 0.3283 (m-40)
  outliers start: 14
  outliers final: 4
  residues processed: 101
  average time/residue: 1.1555
  time to fit residues: 126.9048
Evaluate side-chains
  81 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 HIS
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue 1002 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 50 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 172 HIS
** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.244423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.179745 restraints weight = 11460.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.4069 rms_B_bonded: 2.07
r_work: 0.3873 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3754 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.4187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   9987  Z= 0.160
  Angle     :  0.577  10.793  13533  Z= 0.298
  Chirality :  0.042   0.205   1573
  Planarity :  0.004   0.054   1682
  Dihedral  :  4.455  73.006   1351
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 16.53 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.24), residues: 1218
  helix:  1.77 (0.18), residues: 797
  sheet: -0.48 (0.73), residues: 43
  loop : -1.77 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A1025 
 HIS   0.007   0.001   HIS A 934 
 PHE   0.017   0.001   PHE A 352 
 TYR   0.014   0.002   TYR A1259 
 ARG   0.013   0.001   ARG A 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06501 (  608)
  hydrogen bonds       : angle       3.56451 ( 1806)
  covalent geometry    : bond        0.00327 ( 9987)
  covalent geometry    : angle       0.57720 (13533)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.6045 (pm20) cc_final: 0.5772 (pm20)
REVERT: A  196 ASN cc_start: 0.6471 (OUTLIER) cc_final: 0.6167 (m110)
REVERT: A  231 MET cc_start: 0.7895 (tpp) cc_final: 0.7669 (mmt)
REVERT: A  232 GLU cc_start: 0.7880 (tp30) cc_final: 0.7527 (tt0)
REVERT: A  270 ASP cc_start: 0.6693 (m-30) cc_final: 0.6033 (m-30)
REVERT: A  274 ARG cc_start: 0.7235 (ttp-170) cc_final: 0.6852 (mtp180)
REVERT: A  556 TYR cc_start: 0.5559 (m-80) cc_final: 0.5297 (m-80)
REVERT: A  557 LEU cc_start: 0.6140 (mp) cc_final: 0.5746 (pp)
REVERT: A  730 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8241 (mp)
REVERT: A  834 ASP cc_start: 0.7228 (m-30) cc_final: 0.6984 (t70)
REVERT: A  936 GLU cc_start: 0.6703 (tt0) cc_final: 0.6323 (tt0)
REVERT: A 1002 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7112 (mp0)
REVERT: A 1047 ASN cc_start: 0.3851 (m-40) cc_final: 0.3206 (m-40)
REVERT: A 1157 GLU cc_start: 0.6679 (mp0) cc_final: 0.5790 (tm-30)
REVERT: A 1245 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.5299 (mmm)
  outliers start: 24
  outliers final: 7
  residues processed: 103
  average time/residue: 1.1376
  time to fit residues: 127.4304
Evaluate side-chains
  81 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  196 ASN
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1016 TYR
Chi-restraints excluded: chain A residue 1245 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 108 optimal weight:    4.9990
   chunk 111 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 49 optimal weight:   20.0000
   chunk 55 optimal weight:    6.9990
   chunk 107 optimal weight:    0.8980
   chunk 120 optimal weight:   10.0000
   chunk 52 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0870
   overall best weight:    1.3964

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4789 r_free = 0.4789 target = 0.235870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.168513 restraints weight = 11028.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.4157 rms_B_bonded: 2.34
r_work: 0.3821 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.5420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9987  Z= 0.180
  Angle     :  0.625  12.122  13533  Z= 0.315
  Chirality :  0.043   0.202   1573
  Planarity :  0.004   0.059   1682
  Dihedral  :  4.388  63.072   1351
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.18 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.24), residues: 1218
  helix:  1.60 (0.18), residues: 795
  sheet: -0.47 (0.76), residues: 44
  loop : -1.52 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 947 
 HIS   0.010   0.002   HIS A 153 
 PHE   0.025   0.002   PHE A 336 
 TYR   0.021   0.002   TYR A 339 
 ARG   0.010   0.001   ARG A 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08073 (  608)
  hydrogen bonds       : angle       3.83963 ( 1806)
  covalent geometry    : bond        0.00401 ( 9987)
  covalent geometry    : angle       0.62472 (13533)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 80
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7956 (ttpp)
REVERT: A   65 ASP cc_start: 0.7280 (p0) cc_final: 0.7019 (p0)
REVERT: A  270 ASP cc_start: 0.7286 (m-30) cc_final: 0.6851 (m-30)
REVERT: A  274 ARG cc_start: 0.7655 (ttp-170) cc_final: 0.7272 (mtp180)
REVERT: A  556 TYR cc_start: 0.6200 (m-80) cc_final: 0.5759 (m-80)
REVERT: A  557 LEU cc_start: 0.6522 (mp) cc_final: 0.6136 (pp)
REVERT: A  716 PHE cc_start: 0.7113 (m-80) cc_final: 0.6872 (m-80)
REVERT: A  744 MET cc_start: 0.6695 (tmm) cc_final: 0.6059 (ttm)
REVERT: A  803 GLU cc_start: 0.7476 (tp30) cc_final: 0.6955 (mp0)
REVERT: A  936 GLU cc_start: 0.7438 (tt0) cc_final: 0.6943 (tt0)
REVERT: A  958 MET cc_start: 0.8331 (tpt) cc_final: 0.7856 (ttp)
REVERT: A  972 LYS cc_start: 0.8205 (mttt) cc_final: 0.7942 (mttp)
REVERT: A 1166 MET cc_start: 0.3923 (tpt) cc_final: 0.3684 (tpp)
REVERT: A 1181 GLN cc_start: 0.2838 (OUTLIER) cc_final: 0.2516 (pp30)
  outliers start: 33
  outliers final: 11
  residues processed: 107
  average time/residue: 1.2878
  time to fit residues: 149.0057
Evaluate side-chains
  79 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   32 LYS
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  731 GLN
Chi-restraints excluded: chain A residue  804 SER
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1181 GLN
Chi-restraints excluded: chain A residue 1230 THR
Chi-restraints excluded: chain A residue 1245 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0000
   chunk 121 optimal weight:    9.9990
   chunk 101 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0870
   chunk 114 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 95 optimal weight:    4.9990
   overall best weight:    0.5762

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

Flipped N/Q/H residues before XYZ refinement:
A 196 ASN
** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 931 GLN
** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4815 r_free = 0.4815 target = 0.240345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.170974 restraints weight = 11200.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.4181 rms_B_bonded: 2.78
r_work: 0.3859 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.5588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9987  Z= 0.132
  Angle     :  0.541  12.090  13533  Z= 0.269
  Chirality :  0.040   0.144   1573
  Planarity :  0.004   0.086   1682
  Dihedral  :  4.206  57.989   1351
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.78 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.24), residues: 1218
  helix:  2.06 (0.19), residues: 793
  sheet: -0.29 (0.79), residues: 44
  loop : -1.56 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 947 
 HIS   0.004   0.001   HIS A 934 
 PHE   0.011   0.001   PHE A 352 
 TYR   0.011   0.001   TYR A 155 
 ARG   0.008   0.000   ARG A1189 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06563 (  608)
  hydrogen bonds       : angle       3.61570 ( 1806)
  covalent geometry    : bond        0.00257 ( 9987)
  covalent geometry    : angle       0.54072 (13533)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 72
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 ASP cc_start: 0.7361 (p0) cc_final: 0.6905 (m-30)
REVERT: A   76 GLN cc_start: 0.6740 (pm20) cc_final: 0.6376 (pm20)
REVERT: A  126 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6874 (mtt)
REVERT: A  184 MET cc_start: 0.6517 (mpp) cc_final: 0.6085 (mpt)
REVERT: A  270 ASP cc_start: 0.7293 (m-30) cc_final: 0.6979 (m-30)
REVERT: A  274 ARG cc_start: 0.7588 (ttp-170) cc_final: 0.7219 (mtp180)
REVERT: A  556 TYR cc_start: 0.6260 (m-80) cc_final: 0.5599 (m-80)
REVERT: A  716 PHE cc_start: 0.7051 (m-80) cc_final: 0.6820 (m-80)
REVERT: A  744 MET cc_start: 0.6646 (tmm) cc_final: 0.6106 (ttm)
REVERT: A  803 GLU cc_start: 0.7395 (tp30) cc_final: 0.7013 (mp0)
REVERT: A  936 GLU cc_start: 0.6913 (tt0) cc_final: 0.6534 (tt0)
REVERT: A  958 MET cc_start: 0.8321 (tpt) cc_final: 0.7887 (ttp)
REVERT: A  972 LYS cc_start: 0.8186 (mttt) cc_final: 0.7936 (mttp)
REVERT: A 1002 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7306 (mp0)
REVERT: A 1166 MET cc_start: 0.3958 (tpt) cc_final: 0.3744 (tpp)
  outliers start: 28
  outliers final: 6
  residues processed: 90
  average time/residue: 1.2412
  time to fit residues: 120.9301
Evaluate side-chains
  76 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  122 ASN
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1131 MET
Chi-restraints excluded: chain A residue 1230 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 58 optimal weight:   30.0000
   chunk 83 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 50 optimal weight:   20.0000
   chunk 24 optimal weight:    4.9990
   chunk 96 optimal weight:    3.9990
   chunk 120 optimal weight:    9.9990
   chunk 107 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    3.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 903 HIS
** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.221309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.147390 restraints weight = 11002.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 2.63
r_work: 0.3579 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.7296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.069   9987  Z= 0.316
  Angle     :  0.794  13.389  13533  Z= 0.407
  Chirality :  0.050   0.268   1573
  Planarity :  0.006   0.077   1682
  Dihedral  :  5.098  63.907   1351
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.97 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.23), residues: 1218
  helix:  1.07 (0.18), residues: 785
  sheet: -0.05 (1.02), residues: 30
  loop : -1.61 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A1025 
 HIS   0.016   0.002   HIS A 153 
 PHE   0.038   0.003   PHE A 840 
 TYR   0.027   0.003   TYR A 339 
 ARG   0.010   0.001   ARG A 951 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11433 (  608)
  hydrogen bonds       : angle       4.38047 ( 1806)
  covalent geometry    : bond        0.00756 ( 9987)
  covalent geometry    : angle       0.79379 (13533)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 75
  time to evaluate  : 1.141 
Fit side-chains
REVERT: A   65 ASP cc_start: 0.7423 (p0) cc_final: 0.7032 (m-30)
REVERT: A   76 GLN cc_start: 0.7149 (pm20) cc_final: 0.6766 (pm20)
REVERT: A  270 ASP cc_start: 0.7710 (m-30) cc_final: 0.7309 (m-30)
REVERT: A  274 ARG cc_start: 0.7789 (ttp-170) cc_final: 0.7521 (mtp180)
REVERT: A  556 TYR cc_start: 0.6737 (m-80) cc_final: 0.6165 (m-80)
REVERT: A  716 PHE cc_start: 0.7325 (m-80) cc_final: 0.7121 (m-80)
REVERT: A  744 MET cc_start: 0.7078 (tmm) cc_final: 0.6769 (ttm)
REVERT: A  803 GLU cc_start: 0.7929 (tp30) cc_final: 0.7482 (mp0)
REVERT: A  906 SER cc_start: 0.8234 (t) cc_final: 0.7977 (m)
REVERT: A  958 MET cc_start: 0.8299 (tpt) cc_final: 0.8066 (ttp)
REVERT: A  972 LYS cc_start: 0.8576 (mttt) cc_final: 0.8192 (mttp)
REVERT: A 1131 MET cc_start: 0.4787 (OUTLIER) cc_final: 0.4193 (mmp)
REVERT: A 1166 MET cc_start: 0.4358 (tpt) cc_final: 0.4146 (tpp)
REVERT: A 1212 ASP cc_start: 0.8391 (m-30) cc_final: 0.7984 (m-30)
REVERT: A 1218 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.7094 (mttt)
  outliers start: 37
  outliers final: 12
  residues processed: 105
  average time/residue: 1.1569
  time to fit residues: 132.1089
Evaluate side-chains
  76 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  731 GLN
Chi-restraints excluded: chain A residue  804 SER
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue 1006 MET
Chi-restraints excluded: chain A residue 1020 GLU
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1131 MET
Chi-restraints excluded: chain A residue 1218 LYS
Chi-restraints excluded: chain A residue 1230 THR
Chi-restraints excluded: chain A residue 1245 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9990
   chunk 117 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 43 optimal weight:    6.9990
   chunk 110 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 107 optimal weight:   10.0000
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 196 ASN
** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.226176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.154682 restraints weight = 11134.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 2.70
r_work: 0.3666 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.7256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9987  Z= 0.173
  Angle     :  0.622  11.464  13533  Z= 0.313
  Chirality :  0.042   0.240   1573
  Planarity :  0.005   0.096   1682
  Dihedral  :  4.768  63.157   1351
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 20.66 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.24), residues: 1218
  helix:  1.52 (0.18), residues: 786
  sheet:  0.25 (1.04), residues: 30
  loop : -1.47 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 947 
 HIS   0.007   0.001   HIS A 934 
 PHE   0.027   0.002   PHE A 324 
 TYR   0.015   0.001   TYR A 289 
 ARG   0.007   0.001   ARG A1189 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08710 (  608)
  hydrogen bonds       : angle       4.02790 ( 1806)
  covalent geometry    : bond        0.00362 ( 9987)
  covalent geometry    : angle       0.62178 (13533)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 71
  time to evaluate  : 1.144 
Fit side-chains
REVERT: A   65 ASP cc_start: 0.7417 (p0) cc_final: 0.6961 (m-30)
REVERT: A   76 GLN cc_start: 0.7172 (pm20) cc_final: 0.6746 (pm20)
REVERT: A  126 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6936 (mtm)
REVERT: A  270 ASP cc_start: 0.7596 (m-30) cc_final: 0.7143 (m-30)
REVERT: A  274 ARG cc_start: 0.7733 (ttp-170) cc_final: 0.7406 (mtp180)
REVERT: A  556 TYR cc_start: 0.6714 (m-80) cc_final: 0.6179 (m-80)
REVERT: A  744 MET cc_start: 0.6973 (tmm) cc_final: 0.6683 (ttm)
REVERT: A  803 GLU cc_start: 0.7791 (tp30) cc_final: 0.7319 (mp0)
REVERT: A  936 GLU cc_start: 0.7465 (tt0) cc_final: 0.7171 (tt0)
REVERT: A  958 MET cc_start: 0.8333 (tpt) cc_final: 0.8062 (ttm)
REVERT: A  972 LYS cc_start: 0.8486 (mttt) cc_final: 0.8130 (mttp)
REVERT: A 1131 MET cc_start: 0.4622 (OUTLIER) cc_final: 0.4167 (mmp)
REVERT: A 1166 MET cc_start: 0.4420 (tpt) cc_final: 0.4192 (tpp)
REVERT: A 1197 ILE cc_start: 0.5998 (mp) cc_final: 0.5759 (mp)
REVERT: A 1212 ASP cc_start: 0.8417 (m-30) cc_final: 0.8023 (m-30)
  outliers start: 29
  outliers final: 10
  residues processed: 91
  average time/residue: 1.1220
  time to fit residues: 111.2430
Evaluate side-chains
  77 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  804 SER
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1130 THR
Chi-restraints excluded: chain A residue 1131 MET
Chi-restraints excluded: chain A residue 1230 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 105 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 58 optimal weight:    7.9990
   chunk 118 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 87 optimal weight:    0.5980
   chunk 102 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
A 196 ASN
** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1183 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4728 r_free = 0.4728 target = 0.230410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.162072 restraints weight = 11246.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.4071 rms_B_bonded: 2.46
r_work: 0.3751 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.7191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9987  Z= 0.143
  Angle     :  0.575  11.917  13533  Z= 0.286
  Chirality :  0.041   0.208   1573
  Planarity :  0.004   0.089   1682
  Dihedral  :  4.504  60.430   1351
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 21.41 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.24), residues: 1218
  helix:  1.88 (0.19), residues: 793
  sheet: -0.20 (0.79), residues: 49
  loop : -1.47 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 912 
 HIS   0.006   0.001   HIS A  55 
 PHE   0.015   0.001   PHE A 336 
 TYR   0.015   0.001   TYR A 155 
 ARG   0.009   0.001   ARG A1189 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07195 (  608)
  hydrogen bonds       : angle       3.76438 ( 1806)
  covalent geometry    : bond        0.00282 ( 9987)
  covalent geometry    : angle       0.57510 (13533)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 1.453 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 ASP cc_start: 0.7404 (p0) cc_final: 0.6939 (m-30)
REVERT: A   76 GLN cc_start: 0.7199 (pm20) cc_final: 0.6824 (pm20)
REVERT: A  274 ARG cc_start: 0.7756 (ttp-170) cc_final: 0.7344 (mtp180)
REVERT: A  556 TYR cc_start: 0.6716 (m-80) cc_final: 0.6097 (m-80)
REVERT: A  744 MET cc_start: 0.6893 (tmm) cc_final: 0.6592 (ttm)
REVERT: A  803 GLU cc_start: 0.7573 (tp30) cc_final: 0.7095 (mp0)
REVERT: A  914 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7594 (mt)
REVERT: A  936 GLU cc_start: 0.7331 (tt0) cc_final: 0.6966 (tt0)
REVERT: A  958 MET cc_start: 0.8293 (tpt) cc_final: 0.8085 (tpt)
REVERT: A  972 LYS cc_start: 0.8337 (mttt) cc_final: 0.8070 (mttp)
REVERT: A 1002 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7416 (mp0)
REVERT: A 1131 MET cc_start: 0.4686 (tpt) cc_final: 0.4407 (mmp)
REVERT: A 1157 GLU cc_start: 0.6547 (mp0) cc_final: 0.5860 (tm-30)
REVERT: A 1197 ILE cc_start: 0.5981 (mp) cc_final: 0.5750 (mp)
REVERT: A 1212 ASP cc_start: 0.8353 (m-30) cc_final: 0.7945 (m-30)
  outliers start: 22
  outliers final: 9
  residues processed: 87
  average time/residue: 1.1684
  time to fit residues: 110.6744
Evaluate side-chains
  78 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  804 SER
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1130 THR
Chi-restraints excluded: chain A residue 1230 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 108 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 65 optimal weight:    0.6980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.224682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.157869 restraints weight = 11326.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.4035 rms_B_bonded: 2.53
r_work: 0.3680 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.7414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9987  Z= 0.161
  Angle     :  0.596  11.775  13533  Z= 0.297
  Chirality :  0.042   0.215   1573
  Planarity :  0.004   0.049   1682
  Dihedral  :  4.510  58.092   1351
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 21.97 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.24), residues: 1218
  helix:  1.80 (0.18), residues: 799
  sheet:  0.16 (0.80), residues: 47
  loop : -1.43 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 947 
 HIS   0.006   0.001   HIS A 934 
 PHE   0.024   0.002   PHE A 324 
 TYR   0.021   0.001   TYR A 289 
 ARG   0.005   0.000   ARG A 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07903 (  608)
  hydrogen bonds       : angle       3.82518 ( 1806)
  covalent geometry    : bond        0.00342 ( 9987)
  covalent geometry    : angle       0.59620 (13533)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 1.129 
Fit side-chains
REVERT: A   65 ASP cc_start: 0.7441 (p0) cc_final: 0.6953 (m-30)
REVERT: A   76 GLN cc_start: 0.7146 (pm20) cc_final: 0.6834 (pm20)
REVERT: A  274 ARG cc_start: 0.7765 (ttp-170) cc_final: 0.7372 (mtp180)
REVERT: A  556 TYR cc_start: 0.6716 (m-80) cc_final: 0.6215 (m-80)
REVERT: A  744 MET cc_start: 0.6987 (tmm) cc_final: 0.6704 (ttm)
REVERT: A  803 GLU cc_start: 0.7666 (tp30) cc_final: 0.7152 (mp0)
REVERT: A  936 GLU cc_start: 0.7541 (tt0) cc_final: 0.7159 (tt0)
REVERT: A  958 MET cc_start: 0.8324 (tpt) cc_final: 0.7810 (ttm)
REVERT: A  972 LYS cc_start: 0.8407 (mttt) cc_final: 0.8098 (mttp)
REVERT: A 1002 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7420 (mp0)
REVERT: A 1131 MET cc_start: 0.4856 (OUTLIER) cc_final: 0.4628 (mmp)
REVERT: A 1181 GLN cc_start: 0.2377 (OUTLIER) cc_final: 0.0920 (mm-40)
REVERT: A 1197 ILE cc_start: 0.6038 (mp) cc_final: 0.5806 (mp)
REVERT: A 1212 ASP cc_start: 0.8439 (m-30) cc_final: 0.8063 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 83
  average time/residue: 1.2657
  time to fit residues: 114.8902
Evaluate side-chains
  79 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  804 SER
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1130 THR
Chi-restraints excluded: chain A residue 1131 MET
Chi-restraints excluded: chain A residue 1181 GLN
Chi-restraints excluded: chain A residue 1204 THR
Chi-restraints excluded: chain A residue 1230 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 105 optimal weight:    0.6980
   chunk 44 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.221673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.147381 restraints weight = 11328.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 3.54
r_work: 0.3641 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.7804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9987  Z= 0.178
  Angle     :  0.623  12.425  13533  Z= 0.311
  Chirality :  0.043   0.220   1573
  Planarity :  0.004   0.049   1682
  Dihedral  :  4.561  54.654   1351
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 22.16 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.24), residues: 1218
  helix:  1.70 (0.18), residues: 794
  sheet:  0.18 (0.79), residues: 48
  loop : -1.29 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 947 
 HIS   0.007   0.001   HIS A 153 
 PHE   0.024   0.002   PHE A 336 
 TYR   0.024   0.002   TYR A 289 
 ARG   0.005   0.001   ARG A 951 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08577 (  608)
  hydrogen bonds       : angle       3.90467 ( 1806)
  covalent geometry    : bond        0.00390 ( 9987)
  covalent geometry    : angle       0.62297 (13533)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 1.323 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 ASP cc_start: 0.7363 (p0) cc_final: 0.6881 (m-30)
REVERT: A   76 GLN cc_start: 0.7045 (pm20) cc_final: 0.6714 (pm20)
REVERT: A  274 ARG cc_start: 0.7650 (ttp-170) cc_final: 0.7276 (mtp180)
REVERT: A  556 TYR cc_start: 0.6564 (m-80) cc_final: 0.6038 (m-80)
REVERT: A  803 GLU cc_start: 0.7678 (tp30) cc_final: 0.7181 (mp0)
REVERT: A  936 GLU cc_start: 0.7587 (tt0) cc_final: 0.7069 (tt0)
REVERT: A  958 MET cc_start: 0.8273 (tpt) cc_final: 0.7874 (ttp)
REVERT: A  972 LYS cc_start: 0.8443 (mttt) cc_final: 0.8043 (mttp)
REVERT: A 1002 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7257 (mp0)
REVERT: A 1047 ASN cc_start: 0.5141 (m-40) cc_final: 0.4051 (m-40)
REVERT: A 1157 GLU cc_start: 0.6337 (mp0) cc_final: 0.5720 (tm-30)
REVERT: A 1181 GLN cc_start: 0.2615 (OUTLIER) cc_final: 0.1203 (mm-40)
REVERT: A 1212 ASP cc_start: 0.8517 (m-30) cc_final: 0.8117 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 84
  average time/residue: 1.4253
  time to fit residues: 130.6429
Evaluate side-chains
  82 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 1.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  804 SER
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1118 SER
Chi-restraints excluded: chain A residue 1181 GLN
Chi-restraints excluded: chain A residue 1230 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 67 optimal weight:    0.0070
   chunk 62 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 117 optimal weight:    7.9990
   chunk 83 optimal weight:    3.9990
   chunk 116 optimal weight:    4.9990
   chunk 111 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.9802

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

Flipped N/Q/H residues before XYZ refinement:
** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.223558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.157117 restraints weight = 11284.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 2.30
r_work: 0.3672 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.7855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9987  Z= 0.157
  Angle     :  0.607  11.784  13533  Z= 0.299
  Chirality :  0.042   0.211   1573
  Planarity :  0.004   0.050   1682
  Dihedral  :  4.531  50.505   1351
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 22.16 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.24), residues: 1218
  helix:  1.81 (0.18), residues: 799
  sheet:  0.18 (0.81), residues: 48
  loop : -1.32 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 947 
 HIS   0.006   0.001   HIS A 934 
 PHE   0.028   0.002   PHE A 324 
 TYR   0.017   0.001   TYR A 289 
 ARG   0.006   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07908 (  608)
  hydrogen bonds       : angle       3.83917 ( 1806)
  covalent geometry    : bond        0.00329 ( 9987)
  covalent geometry    : angle       0.60701 (13533)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7024.07 seconds
wall clock time: 122 minutes 35.81 seconds (7355.81 seconds total)