Starting phenix.real_space_refine
on Fri Feb 14 06:31:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iz9_35836/02_2025/8iz9_35836_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iz9_35836/02_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_35836/02_2025/8iz9_35836.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iz9_35836/02_2025/8iz9_35836.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iz9_35836/02_2025/8iz9_35836_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iz9_35836/02_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-5592/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: 6.03, per 1000 atoms: 0.62
  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: 2.75
  Conformation dependent library (CDL) restraints added in 1.2 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: 0.91
  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: 3.36

  Time building geometry restraints manager: 3.13 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:             2.870
  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:             0.020
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.410
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  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:12.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.270
-------------------------------------------------------------------------------
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= 0.141
  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 

*********************** 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  : 0.999 
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: 1.3399
  time to fit residues: 196.9511
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  : 1.047 
-------------------------------------------------------------------------------
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 = 11753.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.4434 rms_B_bonded: 2.24
r_work: 0.4223 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.4103 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6779
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= 0.201
  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 

*********************** 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  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 ILE cc_start: 0.8001 (mt) cc_final: 0.7783 (mp)
REVERT: A  164 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7377 (ttp)
REVERT: A  186 MET cc_start: 0.5079 (tpt) cc_final: 0.4822 (mmm)
REVERT: A  270 ASP cc_start: 0.6454 (m-30) cc_final: 0.5820 (m-30)
REVERT: A  552 ASP cc_start: 0.7264 (m-30) cc_final: 0.6927 (m-30)
REVERT: A  705 PHE cc_start: 0.8045 (m-10) cc_final: 0.7613 (m-10)
REVERT: A  834 ASP cc_start: 0.6907 (m-30) cc_final: 0.6602 (t70)
REVERT: A  912 TRP cc_start: 0.6029 (m-10) cc_final: 0.5520 (m-90)
REVERT: A 1002 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7282 (mp0)
REVERT: A 1015 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7511 (tt0)
REVERT: A 1047 ASN cc_start: 0.3704 (m-40) cc_final: 0.3285 (m-40)
  outliers start: 14
  outliers final: 4
  residues processed: 101
  average time/residue: 1.1465
  time to fit residues: 125.6992
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  : 1.283 
-------------------------------------------------------------------------------
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:    0.0040
   chunk 15 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 56 optimal weight:    0.0070
   chunk 83 optimal weight:    0.9980
   chunk 50 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 88 optimal weight:    0.8980
   overall best weight:    0.5810

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4769 r_free = 0.4769 target = 0.254467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.192186 restraints weight = 11691.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.4176 rms_B_bonded: 2.65
r_work: 0.4028 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3908 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9987  Z= 0.169
  Angle     :  0.526  11.572  13533  Z= 0.265
  Chirality :  0.040   0.161   1573
  Planarity :  0.003   0.049   1682
  Dihedral  :  4.348  71.555   1351
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.81 %
    Favored  : 81.13 %
  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:  1.11 (0.24), residues: 1218
  helix:  1.91 (0.19), residues: 799
  sheet: -0.49 (0.74), residues: 43
  loop : -1.78 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1025 
 HIS   0.007   0.001   HIS A1111 
 PHE   0.013   0.001   PHE A 352 
 TYR   0.011   0.001   TYR A 556 
 ARG   0.005   0.000   ARG A 176 

*********************** 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
  110 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.5969 (pm20) cc_final: 0.5684 (pm20)
REVERT: A  164 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7759 (ttp)
REVERT: A  186 MET cc_start: 0.5510 (tpt) cc_final: 0.5227 (mmm)
REVERT: A  196 ASN cc_start: 0.6341 (OUTLIER) cc_final: 0.6107 (m110)
REVERT: A  232 GLU cc_start: 0.7684 (tp30) cc_final: 0.7482 (tt0)
REVERT: A  270 ASP cc_start: 0.6837 (m-30) cc_final: 0.6285 (m-30)
REVERT: A  556 TYR cc_start: 0.5268 (m-80) cc_final: 0.5007 (m-80)
REVERT: A  557 LEU cc_start: 0.6251 (mp) cc_final: 0.5726 (pp)
REVERT: A  730 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8175 (mp)
REVERT: A  912 TRP cc_start: 0.6246 (m-10) cc_final: 0.5810 (m-90)
REVERT: A 1002 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7442 (mp0)
REVERT: A 1047 ASN cc_start: 0.3711 (m-40) cc_final: 0.3131 (m-40)
  outliers start: 22
  outliers final: 6
  residues processed: 99
  average time/residue: 1.0945
  time to fit residues: 118.0736
Evaluate side-chains
  85 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  164 MET
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 1245 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 108 optimal weight:    0.0020
   chunk 111 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 49 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 107 optimal weight:    2.9990
   chunk 120 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 58 optimal weight:   20.0000
   chunk 33 optimal weight:    0.1980
   overall best weight:    1.1992

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

Flipped N/Q/H residues before XYZ refinement:
A 172 HIS
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.235735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.168004 restraints weight = 11334.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.4160 rms_B_bonded: 3.16
r_work: 0.3844 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3708 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.5351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9987  Z= 0.245
  Angle     :  0.646  12.199  13533  Z= 0.326
  Chirality :  0.043   0.172   1573
  Planarity :  0.004   0.052   1682
  Dihedral  :  4.388  62.444   1351
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 16.90 %
    Favored  : 80.09 %
  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:  0.95 (0.24), residues: 1218
  helix:  1.67 (0.18), residues: 794
  sheet: -0.47 (0.74), residues: 44
  loop : -1.51 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 947 
 HIS   0.010   0.002   HIS A 934 
 PHE   0.023   0.002   PHE A 352 
 TYR   0.020   0.002   TYR A 339 
 ARG   0.006   0.001   ARG A 312 

*********************** 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
  116 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 84
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 MET cc_start: 0.6530 (tpt) cc_final: 0.6329 (mmm)
REVERT: A  196 ASN cc_start: 0.7085 (OUTLIER) cc_final: 0.6794 (m110)
REVERT: A  270 ASP cc_start: 0.7376 (m-30) cc_final: 0.6900 (m-30)
REVERT: A  274 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.7406 (mtp180)
REVERT: A  556 TYR cc_start: 0.5935 (m-80) cc_final: 0.5631 (m-80)
REVERT: A  557 LEU cc_start: 0.6425 (mp) cc_final: 0.6093 (pp)
REVERT: A  716 PHE cc_start: 0.7210 (m-80) cc_final: 0.6966 (m-80)
REVERT: A  744 MET cc_start: 0.6748 (tmm) cc_final: 0.6016 (ttm)
REVERT: A  803 GLU cc_start: 0.7748 (tp30) cc_final: 0.7200 (mp0)
REVERT: A  936 GLU cc_start: 0.7534 (tt0) cc_final: 0.7046 (tt0)
REVERT: A  958 MET cc_start: 0.8457 (tpt) cc_final: 0.7947 (ttp)
REVERT: A  972 LYS cc_start: 0.8343 (mttt) cc_final: 0.7994 (mttp)
REVERT: A 1047 ASN cc_start: 0.3649 (m-40) cc_final: 0.3110 (m-40)
REVERT: A 1166 MET cc_start: 0.3867 (tpt) cc_final: 0.3649 (tpp)
REVERT: A 1181 GLN cc_start: 0.2775 (OUTLIER) cc_final: 0.2382 (pp30)
  outliers start: 32
  outliers final: 10
  residues processed: 105
  average time/residue: 1.2333
  time to fit residues: 139.7729
Evaluate side-chains
  78 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
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  805 ILE
Chi-restraints excluded: chain A residue 1006 MET
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1181 GLN
Chi-restraints excluded: chain A residue 1204 THR
Chi-restraints excluded: chain A residue 1213 GLU
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:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 121 optimal weight:    8.9990
   chunk 101 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 114 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 903 HIS
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 = 0.4787 r_free = 0.4787 target = 0.236245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.165930 restraints weight = 11105.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.4123 rms_B_bonded: 2.65
r_work: 0.3802 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.5864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   9987  Z= 0.227
  Angle     :  0.589  12.702  13533  Z= 0.294
  Chirality :  0.041   0.149   1573
  Planarity :  0.004   0.067   1682
  Dihedral  :  4.393  59.820   1351
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 17.65 %
    Favored  : 78.87 %
  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:  1.17 (0.24), residues: 1218
  helix:  1.90 (0.19), residues: 784
  sheet: -0.20 (0.76), residues: 44
  loop : -1.52 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 947 
 HIS   0.007   0.001   HIS A 153 
 PHE   0.018   0.002   PHE A 336 
 TYR   0.012   0.001   TYR A 155 
 ARG   0.008   0.000   ARG A1189 

*********************** 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
  109 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 72
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASP cc_start: 0.7150 (p0) cc_final: 0.6840 (m-30)
REVERT: A   76 GLN cc_start: 0.6731 (pm20) cc_final: 0.6398 (pm20)
REVERT: A  184 MET cc_start: 0.6592 (mpp) cc_final: 0.6257 (mpt)
REVERT: A  196 ASN cc_start: 0.7065 (OUTLIER) cc_final: 0.6819 (m110)
REVERT: A  270 ASP cc_start: 0.7375 (m-30) cc_final: 0.6941 (m-30)
REVERT: A  274 ARG cc_start: 0.7707 (ttp-170) cc_final: 0.7344 (mtp180)
REVERT: A  556 TYR cc_start: 0.6169 (m-80) cc_final: 0.5620 (m-80)
REVERT: A  716 PHE cc_start: 0.7106 (m-80) cc_final: 0.6891 (m-80)
REVERT: A  744 MET cc_start: 0.6742 (tmm) cc_final: 0.6294 (ttm)
REVERT: A  762 ASN cc_start: 0.7497 (p0) cc_final: 0.7226 (m110)
REVERT: A  803 GLU cc_start: 0.7518 (tp30) cc_final: 0.7165 (mp0)
REVERT: A  906 SER cc_start: 0.7858 (t) cc_final: 0.7565 (m)
REVERT: A  936 GLU cc_start: 0.7200 (tt0) cc_final: 0.6995 (tt0)
REVERT: A  958 MET cc_start: 0.8294 (tpt) cc_final: 0.7915 (ttp)
REVERT: A  972 LYS cc_start: 0.8286 (mttt) cc_final: 0.8024 (mttp)
REVERT: A 1002 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7245 (mp0)
REVERT: A 1049 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6397 (mpt)
REVERT: A 1112 ASP cc_start: 0.6693 (t70) cc_final: 0.6482 (t0)
REVERT: A 1166 MET cc_start: 0.3979 (tpt) cc_final: 0.3699 (tpp)
  outliers start: 37
  outliers final: 12
  residues processed: 101
  average time/residue: 1.2469
  time to fit residues: 136.9474
Evaluate side-chains
  85 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
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  154 LEU
Chi-restraints excluded: chain A residue  196 ASN
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  731 GLN
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  823 ASN
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1049 MET
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1131 MET
Chi-restraints excluded: chain A residue 1204 THR
Chi-restraints excluded: chain A residue 1230 THR
Chi-restraints excluded: chain A residue 1245 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 58 optimal weight:    9.9990
   chunk 83 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 50 optimal weight:   20.0000
   chunk 24 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9990
   chunk 120 optimal weight:    9.9990
   chunk 107 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A  35 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 = 0.4577 r_free = 0.4577 target = 0.220249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.141849 restraints weight = 11201.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3859 rms_B_bonded: 3.38
r_work: 0.3599 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.7255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   9987  Z= 0.382
  Angle     :  0.733  12.684  13533  Z= 0.377
  Chirality :  0.048   0.243   1573
  Planarity :  0.005   0.085   1682
  Dihedral  :  4.905  62.659   1351
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.22 %
    Favored  : 78.31 %
  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:  0.47 (0.24), residues: 1218
  helix:  1.18 (0.18), residues: 789
  sheet:  0.62 (0.89), residues: 35
  loop : -1.51 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A1025 
 HIS   0.015   0.002   HIS A 153 
 PHE   0.033   0.003   PHE A 840 
 TYR   0.025   0.002   TYR A 137 
 ARG   0.011   0.001   ARG A1189 

*********************** 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
  114 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 77
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.7005 (pm20) cc_final: 0.6635 (pm20)
REVERT: A  196 ASN cc_start: 0.7419 (OUTLIER) cc_final: 0.7131 (m110)
REVERT: A  270 ASP cc_start: 0.7490 (m-30) cc_final: 0.7031 (m-30)
REVERT: A  274 ARG cc_start: 0.7703 (ttp-170) cc_final: 0.7430 (mtp180)
REVERT: A  556 TYR cc_start: 0.6534 (m-80) cc_final: 0.6063 (m-80)
REVERT: A  744 MET cc_start: 0.6931 (tmm) cc_final: 0.6653 (ttm)
REVERT: A  906 SER cc_start: 0.7989 (t) cc_final: 0.7756 (m)
REVERT: A  958 MET cc_start: 0.8282 (tpt) cc_final: 0.8027 (ttp)
REVERT: A  972 LYS cc_start: 0.8532 (mttt) cc_final: 0.8105 (mttp)
REVERT: A 1131 MET cc_start: 0.4475 (OUTLIER) cc_final: 0.3966 (mmp)
REVERT: A 1166 MET cc_start: 0.4287 (tpt) cc_final: 0.4076 (tpp)
REVERT: A 1181 GLN cc_start: 0.3138 (OUTLIER) cc_final: 0.2846 (pp30)
REVERT: A 1197 ILE cc_start: 0.5901 (mp) cc_final: 0.5658 (mp)
REVERT: A 1212 ASP cc_start: 0.8340 (m-30) cc_final: 0.7890 (m-30)
REVERT: A 1218 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7175 (mttt)
  outliers start: 37
  outliers final: 11
  residues processed: 104
  average time/residue: 1.1988
  time to fit residues: 135.2643
Evaluate side-chains
  83 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  196 ASN
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  731 GLN
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  975 ASP
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1131 MET
Chi-restraints excluded: chain A residue 1181 GLN
Chi-restraints excluded: chain A residue 1218 LYS
Chi-restraints excluded: chain A residue 1230 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 117 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 8 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   chunk 110 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0870
   chunk 107 optimal weight:    0.7980
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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 = 0.4632 r_free = 0.4632 target = 0.226693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.160728 restraints weight = 11361.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 2.59
r_work: 0.3739 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3605 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.7090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9987  Z= 0.189
  Angle     :  0.586  11.317  13533  Z= 0.294
  Chirality :  0.041   0.237   1573
  Planarity :  0.004   0.072   1682
  Dihedral  :  4.558  57.383   1351
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 19.91 %
    Favored  : 77.65 %
  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:  1.09 (0.24), residues: 1218
  helix:  1.70 (0.19), residues: 795
  sheet:  0.75 (0.89), residues: 35
  loop : -1.40 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 947 
 HIS   0.005   0.001   HIS A 152 
 PHE   0.029   0.001   PHE A 324 
 TYR   0.015   0.001   TYR A 155 
 ARG   0.005   0.000   ARG A1189 

*********************** 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
  101 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 1.136 
Fit side-chains
REVERT: A   76 GLN cc_start: 0.7034 (pm20) cc_final: 0.6643 (pm20)
REVERT: A  196 ASN cc_start: 0.7375 (OUTLIER) cc_final: 0.7062 (m110)
REVERT: A  274 ARG cc_start: 0.7882 (ttp-170) cc_final: 0.7483 (mtp180)
REVERT: A  556 TYR cc_start: 0.6769 (m-80) cc_final: 0.6129 (m-80)
REVERT: A  744 MET cc_start: 0.7113 (tmm) cc_final: 0.6820 (ttm)
REVERT: A  803 GLU cc_start: 0.8023 (tp30) cc_final: 0.7350 (mp0)
REVERT: A  936 GLU cc_start: 0.7445 (tt0) cc_final: 0.6981 (tt0)
REVERT: A  958 MET cc_start: 0.8478 (tpt) cc_final: 0.8105 (ttm)
REVERT: A  972 LYS cc_start: 0.8503 (mttt) cc_final: 0.8152 (mttp)
REVERT: A 1049 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6684 (mpp)
REVERT: A 1131 MET cc_start: 0.4863 (OUTLIER) cc_final: 0.4356 (mmp)
REVERT: A 1166 MET cc_start: 0.4321 (tpt) cc_final: 0.4112 (tpp)
REVERT: A 1181 GLN cc_start: 0.3320 (OUTLIER) cc_final: 0.2797 (pp30)
REVERT: A 1197 ILE cc_start: 0.6161 (mp) cc_final: 0.5951 (mp)
REVERT: A 1212 ASP cc_start: 0.8448 (m-30) cc_final: 0.8064 (m-30)
  outliers start: 26
  outliers final: 7
  residues processed: 91
  average time/residue: 1.2181
  time to fit residues: 120.1790
Evaluate side-chains
  79 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  196 ASN
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue 1049 MET
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 1230 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 105 optimal weight:    0.4980
   chunk 13 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 118 optimal weight:    7.9990
   chunk 47 optimal weight:    0.4980
   chunk 87 optimal weight:    0.4980
   chunk 102 optimal weight:    4.9990
   chunk 32 optimal weight:    0.2980
   chunk 75 optimal weight:    0.9980
   chunk 57 optimal weight:   10.0000
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.4656 r_free = 0.4656 target = 0.229721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.163566 restraints weight = 11500.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.4088 rms_B_bonded: 2.58
r_work: 0.3789 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3654 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.7032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9987  Z= 0.168
  Angle     :  0.566  12.807  13533  Z= 0.281
  Chirality :  0.040   0.208   1573
  Planarity :  0.004   0.098   1682
  Dihedral  :  4.408  56.463   1351
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 21.03 %
    Favored  : 77.28 %
  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:  1.39 (0.24), residues: 1218
  helix:  2.01 (0.19), residues: 790
  sheet:  0.74 (0.82), residues: 42
  loop : -1.44 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 947 
 HIS   0.005   0.001   HIS A  35 
 PHE   0.013   0.001   PHE A 352 
 TYR   0.012   0.001   TYR A 155 
 ARG   0.007   0.000   ARG A1189 

*********************** 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
  88 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.7014 (pm20) cc_final: 0.6593 (pm20)
REVERT: A  274 ARG cc_start: 0.7810 (ttp-170) cc_final: 0.7378 (mtp180)
REVERT: A  556 TYR cc_start: 0.6684 (m-80) cc_final: 0.6067 (m-80)
REVERT: A  744 MET cc_start: 0.7056 (tmm) cc_final: 0.6744 (ttm)
REVERT: A  803 GLU cc_start: 0.7884 (tp30) cc_final: 0.7181 (mp0)
REVERT: A  936 GLU cc_start: 0.7391 (tt0) cc_final: 0.6902 (tt0)
REVERT: A  972 LYS cc_start: 0.8420 (mttt) cc_final: 0.8067 (mttp)
REVERT: A 1131 MET cc_start: 0.4944 (tpt) cc_final: 0.4534 (mmp)
REVERT: A 1134 ASN cc_start: 0.6361 (t0) cc_final: 0.6042 (t0)
REVERT: A 1157 GLU cc_start: 0.6721 (mp0) cc_final: 0.5738 (tm-30)
REVERT: A 1166 MET cc_start: 0.4315 (tpt) cc_final: 0.4115 (tpp)
REVERT: A 1181 GLN cc_start: 0.3276 (OUTLIER) cc_final: 0.2794 (pp30)
REVERT: A 1197 ILE cc_start: 0.6075 (mp) cc_final: 0.5873 (mp)
REVERT: A 1212 ASP cc_start: 0.8435 (m-30) cc_final: 0.8023 (m-30)
REVERT: A 1245 MET cc_start: 0.6792 (mpt) cc_final: 0.6582 (mpt)
  outliers start: 18
  outliers final: 8
  residues processed: 83
  average time/residue: 1.2345
  time to fit residues: 111.1278
Evaluate side-chains
  76 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
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  805 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 108 optimal weight:    0.0000
   chunk 80 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0870
   chunk 31 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   overall best weight:    0.4962

-------------------------------------------------------------------------------
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 = 0.4664 r_free = 0.4664 target = 0.230772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.163243 restraints weight = 11424.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.4091 rms_B_bonded: 3.19
r_work: 0.3807 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3670 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.7037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9987  Z= 0.169
  Angle     :  0.555  12.674  13533  Z= 0.275
  Chirality :  0.040   0.215   1573
  Planarity :  0.003   0.049   1682
  Dihedral  :  4.286  49.740   1351
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 21.22 %
    Favored  : 77.00 %
  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:  1.62 (0.25), residues: 1218
  helix:  2.18 (0.19), residues: 791
  sheet:  0.54 (0.79), residues: 48
  loop : -1.32 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 947 
 HIS   0.005   0.001   HIS A  35 
 PHE   0.029   0.001   PHE A 324 
 TYR   0.010   0.001   TYR A 155 
 ARG   0.003   0.000   ARG A 951 

*********************** 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
  87 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.6943 (pm20) cc_final: 0.6599 (pm20)
REVERT: A  556 TYR cc_start: 0.6733 (m-80) cc_final: 0.6125 (m-80)
REVERT: A  744 MET cc_start: 0.7062 (tmm) cc_final: 0.6749 (ttm)
REVERT: A  803 GLU cc_start: 0.7764 (tp30) cc_final: 0.7125 (mp0)
REVERT: A  936 GLU cc_start: 0.7310 (tt0) cc_final: 0.6816 (tt0)
REVERT: A  958 MET cc_start: 0.8378 (tpt) cc_final: 0.7708 (ttm)
REVERT: A  972 LYS cc_start: 0.8414 (mttt) cc_final: 0.8074 (mttp)
REVERT: A 1126 LEU cc_start: 0.7192 (mp) cc_final: 0.6862 (tt)
REVERT: A 1131 MET cc_start: 0.4806 (tpt) cc_final: 0.4528 (mmp)
REVERT: A 1157 GLU cc_start: 0.6586 (mp0) cc_final: 0.5635 (tm-30)
REVERT: A 1181 GLN cc_start: 0.3223 (OUTLIER) cc_final: 0.2751 (pp30)
REVERT: A 1212 ASP cc_start: 0.8447 (m-30) cc_final: 0.8019 (m-30)
  outliers start: 19
  outliers final: 9
  residues processed: 82
  average time/residue: 1.1463
  time to fit residues: 103.0195
Evaluate side-chains
  76 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
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  805 ILE
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1118 SER
Chi-restraints excluded: chain A residue 1130 THR
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 77 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 105 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.4575 r_free = 0.4575 target = 0.220470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.152193 restraints weight = 11322.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 2.68
r_work: 0.3635 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3496 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.7759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   9987  Z= 0.351
  Angle     :  0.683  13.778  13533  Z= 0.343
  Chirality :  0.045   0.227   1573
  Planarity :  0.004   0.062   1682
  Dihedral  :  4.562  45.258   1351
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 21.69 %
    Favored  : 77.09 %
  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:  0.98 (0.24), residues: 1218
  helix:  1.56 (0.18), residues: 793
  sheet:  0.49 (0.79), residues: 48
  loop : -1.32 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 947 
 HIS   0.012   0.002   HIS A 153 
 PHE   0.025   0.002   PHE A 352 
 TYR   0.022   0.002   TYR A 339 
 ARG   0.006   0.001   ARG A 951 

********************** 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
  84 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 1.162 
Fit side-chains
REVERT: A   76 GLN cc_start: 0.6976 (pm20) cc_final: 0.6687 (pm20)
REVERT: A  196 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.7198 (m110)
REVERT: A  274 ARG cc_start: 0.7849 (ttp-170) cc_final: 0.7495 (mtp180)
REVERT: A  556 TYR cc_start: 0.6862 (m-80) cc_final: 0.6377 (m-80)
REVERT: A  744 MET cc_start: 0.7149 (tmm) cc_final: 0.6920 (ttm)
REVERT: A  803 GLU cc_start: 0.8141 (tp30) cc_final: 0.7564 (mp0)
REVERT: A  958 MET cc_start: 0.8541 (tpt) cc_final: 0.8017 (ttp)
REVERT: A  972 LYS cc_start: 0.8593 (mttt) cc_final: 0.8200 (mttp)
REVERT: A 1047 ASN cc_start: 0.5101 (m-40) cc_final: 0.3984 (m-40)
REVERT: A 1131 MET cc_start: 0.5364 (tpt) cc_final: 0.4999 (mmp)
REVERT: A 1181 GLN cc_start: 0.3486 (OUTLIER) cc_final: 0.2946 (pp30)
  outliers start: 13
  outliers final: 9
  residues processed: 81
  average time/residue: 1.1542
  time to fit residues: 101.9708
Evaluate side-chains
  77 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
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  196 ASN
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  975 ASP
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1130 THR
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:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 85 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 114 optimal weight:    7.9990
   chunk 117 optimal weight:   10.0000
   chunk 83 optimal weight:    0.5980
   chunk 116 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4618 r_free = 0.4618 target = 0.225427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.157120 restraints weight = 11282.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.4027 rms_B_bonded: 3.20
r_work: 0.3727 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3590 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.7677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9987  Z= 0.195
  Angle     :  0.584  12.887  13533  Z= 0.291
  Chirality :  0.041   0.201   1573
  Planarity :  0.004   0.055   1682
  Dihedral  :  4.334  42.911   1351
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 21.69 %
    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:  1.32 (0.24), residues: 1218
  helix:  1.87 (0.19), residues: 798
  sheet:  0.57 (0.80), residues: 48
  loop : -1.33 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 947 
 HIS   0.005   0.001   HIS A  35 
 PHE   0.015   0.001   PHE A 352 
 TYR   0.014   0.001   TYR A 155 
 ARG   0.003   0.000   ARG A 951 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7569.40 seconds
wall clock time: 134 minutes 10.26 seconds (8050.26 seconds total)