Starting phenix.real_space_refine
on Tue Mar  3 20:51:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jlu_22380/03_2026/7jlu_22380.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jlu_22380/03_2026/7jlu_22380.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jlu_22380/03_2026/7jlu_22380.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jlu_22380/03_2026/7jlu_22380.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jlu_22380/03_2026/7jlu_22380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jlu_22380/03_2026/7jlu_22380.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      52      5.16       5
     C    5499      2.51       5
     N    1460      2.21       5
     O    1580      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 100 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8592
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 726, 5884
          Classifications: {'peptide': 726}
          Link IDs: {'PTRANS': 31, 'TRANS': 694}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 353, 2707
          Classifications: {'peptide': 353}
          Link IDs: {'PTRANS': 24, 'TRANS': 328}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.12, per 1000 atoms: 0.25
  Number of scatterers: 8592
  At special positions: 0
  Unit cell: (96.6758, 108.878, 94.7986, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      52     16.00
     O    1580      8.00
     N    1460      7.00
     C    5499      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 326.8 milliseconds
  

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2052

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 5 sheets defined
      31.7% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 540 through 546
      removed outlier: 3.885A  pdb=" N   TYR A 546 " --> pdb=" O   LEU A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 554
    Processing helix  chain 'A' and resid 663 through 669
      removed outlier: 3.549A  pdb=" N   LEU A 669 " --> pdb=" O   VAL A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 742
      removed outlier: 3.853A  pdb=" N   ILE A 736 " --> pdb=" O   PRO A 733 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   GLU A 737 " --> pdb=" O   ALA A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 763
    Processing helix  chain 'A' and resid 803 through 808
      removed outlier: 3.638A  pdb=" N   ASN A 806 " --> pdb=" O   SER A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 831
      removed outlier: 3.658A  pdb=" N   GLY A 830 " --> pdb=" O   SER A 827 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LEU A 831 " --> pdb=" O   ILE A 828 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 827 through 831'
    Processing helix  chain 'A' and resid 896 through 901
      removed outlier: 3.827A  pdb=" N   ILE A 899 " --> pdb=" O   PRO A 896 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 945 through 949
      removed outlier: 3.520A  pdb=" N   LEU A 949 " --> pdb=" O   VAL A 946 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 976
      removed outlier: 3.855A  pdb=" N   LEU A 976 " --> pdb=" O   SER A 972 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 977 through 981
    Processing helix  chain 'A' and resid 1044 through 1052
      removed outlier: 3.590A  pdb=" N   MET A1048 " --> pdb=" O   ALA A1044 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLU A1049 " --> pdb=" O   LEU A1045 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1072
      removed outlier: 4.007A  pdb=" N   TYR A1072 " --> pdb=" O   TYR A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1075 through 1079
      removed outlier: 3.570A  pdb=" N   ILE A1078 " --> pdb=" O   LEU A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1083 through 1100
      removed outlier: 4.271A  pdb=" N   GLU A1087 " --> pdb=" O   SER A1083 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ASN A1088 " --> pdb=" O   GLU A1084 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLN A1090 " --> pdb=" O   LEU A1086 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   GLN A1092 " --> pdb=" O   ASN A1088 " (cutoff:3.500A)
      removed outlier: 5.084A  pdb=" N   GLN A1093 " --> pdb=" O   SER A1089 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP A1095 " --> pdb=" O   LYS A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1149
      removed outlier: 4.141A  pdb=" N   THR A1148 " --> pdb=" O   TYR A1145 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   GLU A1149 " --> pdb=" O   TRP A1146 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1145 through 1149'
    Processing helix  chain 'A' and resid 1166 through 1178
      removed outlier: 3.629A  pdb=" N   ASP A1170 " --> pdb=" O   ALA A1166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1183 through 1190
      removed outlier: 3.716A  pdb=" N   GLU A1189 " --> pdb=" O   TYR A1186 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   TYR A1190 " --> pdb=" O   TRP A1187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 103
    Processing helix  chain 'B' and resid 121 through 136
      removed outlier: 3.706A  pdb=" N   VAL B 125 " --> pdb=" O   PRO B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 168
    Processing helix  chain 'B' and resid 184 through 192
    Processing helix  chain 'B' and resid 195 through 199
      removed outlier: 3.517A  pdb=" N   GLY B 198 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 223
      removed outlier: 3.570A  pdb=" N   GLU B 218 " --> pdb=" O   ARG B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 243
    Processing helix  chain 'B' and resid 245 through 252
    Processing helix  chain 'B' and resid 278 through 284
      removed outlier: 4.160A  pdb=" N   ASP B 284 " --> pdb=" O   ASN B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 298
    Processing helix  chain 'B' and resid 308 through 313
    Processing helix  chain 'B' and resid 317 through 325
      removed outlier: 3.600A  pdb=" N   GLU B 321 " --> pdb=" O   PRO B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 350
      removed outlier: 3.656A  pdb=" N   GLN B 350 " --> pdb=" O   TRP B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 353
      No H-bonds generated for 'chain 'B' and resid 351 through 353'
    Processing helix  chain 'B' and resid 358 through 366
    Processing helix  chain 'B' and resid 384 through 389
    Processing helix  chain 'B' and resid 390 through 392
      No H-bonds generated for 'chain 'B' and resid 390 through 392'
    Processing helix  chain 'B' and resid 398 through 407
      removed outlier: 3.911A  pdb=" N   THR B 402 " --> pdb=" O   TYR B 398 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 415
      removed outlier: 3.895A  pdb=" N   ARG B 412 " --> pdb=" O   PRO B 408 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   LEU B 413 " --> pdb=" O   GLY B 409 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU B 414 " --> pdb=" O   ALA B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 452
    Processing sheet with id=AA1, first strand: chain 'A' and resid 529 through 531
      removed outlier: 3.625A  pdb=" N   LEU A 529 " --> pdb=" O   ILE A 559 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A 561 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A 531 " --> pdb=" O   VAL A 561 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU A 560 " --> pdb=" O   GLU A 584 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   LEU A 605 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   SER A 631 " --> pdb=" O   LEU A 605 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   MET A 607 " --> pdb=" O   SER A 631 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 689 through 690
      removed outlier: 3.805A  pdb=" N   ILE A 690 " --> pdb=" O   GLU A 711 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 744 through 748
      removed outlier: 7.046A  pdb=" N   VAL A 795 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU A 790 " --> pdb=" O   GLU A 814 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   CYS A 816 " --> pdb=" O   LEU A 790 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LEU A 792 " --> pdb=" O   CYS A 816 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LEU A 813 " --> pdb=" O   LYS A 838 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   LEU A 840 " --> pdb=" O   LEU A 813 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ILE A 815 " --> pdb=" O   LEU A 840 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ILE A 884 " --> pdb=" O   CYS A 909 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   SER A 911 " --> pdb=" O   ILE A 884 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   MET A 886 " --> pdb=" O   SER A 911 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ASP A1040 " --> pdb=" O   ILE A1018 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   HIS A1120 " --> pdb=" O   VAL A1063 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A1238 " --> pdb=" O   PHE A1162 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   PHE A1162 " --> pdb=" O   VAL A1238 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   PHE A1246 " --> pdb=" O   PHE A1154 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   PHE A1154 " --> pdb=" O   PHE A1246 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   GLY A1153 " --> pdb=" O   VAL A1289 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   VAL A1289 " --> pdb=" O   GLY A1153 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ALA A1155 " --> pdb=" O   ASN A1287 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ASN A1287 " --> pdb=" O   ALA A1155 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1139 through 1140
      removed outlier: 3.590A  pdb=" N   CYS A1271 " --> pdb=" O   THR A1206 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LYS A1223 " --> pdb=" O   ALA A1207 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 174 through 176
      removed outlier: 5.398A  pdb=" N   LEU B 109 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 5.287A  pdb=" N   LEU B 141 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   THR B 111 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   ASP B 143 " --> pdb=" O   THR B 111 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ASP B 110 " --> pdb=" O   GLY B 228 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   VAL B 230 " --> pdb=" O   ASP B 110 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   LEU B 112 " --> pdb=" O   VAL B 230 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   LEU B 227 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ILE B 256 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   MET B 229 " --> pdb=" O   ILE B 256 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   ILE B 258 " --> pdb=" O   MET B 229 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   VAL B 231 " --> pdb=" O   ILE B 258 " (cutoff:3.500A)
      removed outlier: 8.399A  pdb=" N   ARG B 303 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   ILE B 256 " --> pdb=" O   ARG B 303 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   LEU B 305 " --> pdb=" O   ILE B 256 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ILE B 258 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   LEU B 302 " --> pdb=" O   GLU B 429 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   VAL B 431 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ILE B 304 " --> pdb=" O   VAL B 431 " (cutoff:3.500A)

    263 hydrogen bonds defined for protein.
    699 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.37

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2793
        1.34 -     1.46: 1911
        1.46 -     1.58: 3998
        1.58 -     1.70: 0
        1.70 -     1.82: 78
  Bond restraints: 8780
  Sorted by residual:
  bond pdb=" N   THR A1136 "
       pdb=" CA  THR A1136 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.20e+00
  bond pdb=" CA  THR B 147 "
       pdb=" C   THR B 147 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.012 1.24e-02 6.50e+03 8.96e-01
  bond pdb=" CB  GLU B 251 "
       pdb=" CG  GLU B 251 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.43e-01
  bond pdb=" CA  ASN A 744 "
       pdb=" CB  ASN A 744 "
    ideal  model  delta    sigma   weight residual
    1.535  1.554 -0.019 2.09e-02 2.29e+03 8.33e-01
  bond pdb=" CB  ASP B 150 "
       pdb=" CG  ASP B 150 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.91e-01
  ... (remaining 8775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 11613
        2.30 -     4.59: 257
        4.59 -     6.89: 28
        6.89 -     9.19: 6
        9.19 -    11.49: 1
  Bond angle restraints: 11905
  Sorted by residual:
  angle pdb=" CA  LEU B 334 "
        pdb=" CB  LEU B 334 "
        pdb=" CG  LEU B 334 "
      ideal   model   delta    sigma   weight residual
     116.30  127.79  -11.49 3.50e+00 8.16e-02 1.08e+01
  angle pdb=" CA  GLU B 251 "
        pdb=" CB  GLU B 251 "
        pdb=" CG  GLU B 251 "
      ideal   model   delta    sigma   weight residual
     114.10  120.41   -6.31 2.00e+00 2.50e-01 9.95e+00
  angle pdb=" CB  MET A1241 "
        pdb=" CG  MET A1241 "
        pdb=" SD  MET A1241 "
      ideal   model   delta    sigma   weight residual
     112.70  120.82   -8.12 3.00e+00 1.11e-01 7.33e+00
  angle pdb=" CB  MET B 383 "
        pdb=" CG  MET B 383 "
        pdb=" SD  MET B 383 "
      ideal   model   delta    sigma   weight residual
     112.70  120.76   -8.06 3.00e+00 1.11e-01 7.22e+00
  angle pdb=" C   ALA B 351 "
        pdb=" N   ASN B 352 "
        pdb=" CA  ASN B 352 "
      ideal   model   delta    sigma   weight residual
     121.54  126.63   -5.09 1.91e+00 2.74e-01 7.09e+00
  ... (remaining 11900 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4548
       17.96 -    35.92: 634
       35.92 -    53.89: 117
       53.89 -    71.85: 18
       71.85 -    89.81: 7
  Dihedral angle restraints: 5324
    sinusoidal: 2162
      harmonic: 3162
  Sorted by residual:
  dihedral pdb=" CA  SER A 590 "
           pdb=" C   SER A 590 "
           pdb=" N   ASN A 591 "
           pdb=" CA  ASN A 591 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.98  -22.02     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  TRP A 900 "
           pdb=" C   TRP A 900 "
           pdb=" N   MET A 901 "
           pdb=" CA  MET A 901 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.61   19.39     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  ARG A1133 "
           pdb=" C   ARG A1133 "
           pdb=" N   SER A1134 "
           pdb=" CA  SER A1134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.87  -19.13     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 5321 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 777
       0.033 -    0.066: 367
       0.066 -    0.099: 137
       0.099 -    0.131: 60
       0.131 -    0.164: 9
  Chirality restraints: 1350
  Sorted by residual:
  chirality pdb=" CA  GLU A 743 "
            pdb=" N   GLU A 743 "
            pdb=" C   GLU A 743 "
            pdb=" CB  GLU A 743 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.74e-01
  chirality pdb=" CG  LEU A 630 "
            pdb=" CB  LEU A 630 "
            pdb=" CD1 LEU A 630 "
            pdb=" CD2 LEU A 630 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.35e-01
  chirality pdb=" CB  THR A1299 "
            pdb=" CA  THR A1299 "
            pdb=" OG1 THR A1299 "
            pdb=" CG2 THR A1299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.56e-01
  ... (remaining 1347 not shown)

  Planarity restraints: 1515
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 900 "    0.017 2.00e-02 2.50e+03   1.46e-02 5.32e+00
        pdb=" CG  TRP A 900 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 900 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 900 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 900 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 900 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 900 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 900 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 900 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 900 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 800 "   -0.029 5.00e-02 4.00e+02   4.34e-02 3.01e+00
        pdb=" N   PRO A 801 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 801 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 801 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 385 "   -0.006 2.00e-02 2.50e+03   1.22e-02 2.59e+00
        pdb=" CG  PHE B 385 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 385 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 385 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 385 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 385 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 385 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1512 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 475
        2.73 -     3.27: 8625
        3.27 -     3.81: 13132
        3.81 -     4.36: 15685
        4.36 -     4.90: 26632
  Nonbonded interactions: 64549
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1080 "
            pdb=" OD1 ASP A1081 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" O   LEU A 551 "
            pdb=" OG1 THR A 554 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OD1 ASP A1040 "
            pdb=" N   GLU A1041 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   GLU A 543 "
            pdb=" OG  SER A 547 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG1 THR B 418 "
            pdb=" OE1 GLU B 435 "
     model   vdw
     2.269 3.040
  ... (remaining 64544 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.730
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.180
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8780  Z= 0.144
  Angle     :  0.780  11.487  11905  Z= 0.392
  Chirality :  0.046   0.164   1350
  Planarity :  0.004   0.043   1515
  Dihedral  : 16.633  89.810   3272
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.28 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.42 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.26), residues: 1067
  helix:  0.08 (0.35), residues: 246
  sheet:  0.28 (0.37), residues: 203
  loop : -2.08 (0.24), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 882 
 TYR   0.020   0.002   TYR A1186 
 PHE   0.026   0.002   PHE B 385 
 TRP   0.040   0.002   TRP A 900 
 HIS   0.008   0.001   HIS B 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8780)
  covalent geometry    : angle       0.77959 (11905)
  hydrogen bonds       : bond        0.19420 (  263)
  hydrogen bonds       : angle       6.92520 (  699)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A  551 LEU cc_start: 0.7731 (mm) cc_final: 0.7459 (mt)
REVERT: A  586 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7289 (mtp180)
REVERT: A  607 MET cc_start: 0.6621 (mmm) cc_final: 0.6395 (mtt)
REVERT: A  677 MET cc_start: 0.8015 (mmt) cc_final: 0.7814 (mmt)
REVERT: A 1138 MET cc_start: 0.7502 (ttt) cc_final: 0.7211 (ttt)
  outliers start: 2
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0787
  time to fit residues: 11.7601
Evaluate side-chains
  84 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  586 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.0770
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.1742

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

Flipped N/Q/H residues before XYZ refinement:
** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 286 HIS
B 328 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.115486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.102871 restraints weight = 18612.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.105442 restraints weight = 9861.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.107157 restraints weight = 6181.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.108320 restraints weight = 4331.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.109066 restraints weight = 3289.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8780  Z= 0.148
  Angle     :  0.663   7.136  11905  Z= 0.334
  Chirality :  0.046   0.163   1350
  Planarity :  0.005   0.049   1515
  Dihedral  :  5.079  31.790   1177
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.28 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 11.79 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.54 (0.26), residues: 1067
  helix: -0.09 (0.33), residues: 252
  sheet:  0.16 (0.37), residues: 216
  loop : -1.98 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1233 
 TYR   0.015   0.002   TYR A1145 
 PHE   0.021   0.002   PHE A 704 
 TRP   0.017   0.002   TRP A 582 
 HIS   0.005   0.001   HIS B 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8780)
  covalent geometry    : angle       0.66328 (11905)
  hydrogen bonds       : bond        0.04693 (  263)
  hydrogen bonds       : angle       5.60062 (  699)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  677 MET cc_start: 0.8191 (mmt) cc_final: 0.7815 (mmt)
REVERT: A 1040 ASP cc_start: 0.8525 (t0) cc_final: 0.8279 (t0)
REVERT: B  107 LEU cc_start: 0.7588 (mp) cc_final: 0.7326 (mt)
  outliers start: 11
  outliers final: 7
  residues processed: 89
  average time/residue: 0.0676
  time to fit residues: 9.2992
Evaluate side-chains
  86 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  718 HIS
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue 1246 PHE
Chi-restraints excluded: chain B residue  148 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:    8.9990
   chunk 73 optimal weight:    0.0980
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 32 optimal weight:    0.3980
   chunk 102 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.5582

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

Flipped N/Q/H residues before XYZ refinement:
A 751 ASN
** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.117534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.104895 restraints weight = 18523.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.107555 restraints weight = 9753.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.109293 restraints weight = 6014.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.110471 restraints weight = 4181.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.111280 restraints weight = 3159.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8780  Z= 0.104
  Angle     :  0.585   5.827  11905  Z= 0.295
  Chirality :  0.044   0.143   1350
  Planarity :  0.004   0.049   1515
  Dihedral  :  4.586  21.334   1173
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.05 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.26), residues: 1067
  helix:  0.15 (0.34), residues: 253
  sheet:  0.23 (0.37), residues: 214
  loop : -2.00 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 621 
 TYR   0.013   0.001   TYR A1145 
 PHE   0.018   0.001   PHE A 704 
 TRP   0.020   0.001   TRP A 900 
 HIS   0.003   0.001   HIS A1279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 8780)
  covalent geometry    : angle       0.58539 (11905)
  hydrogen bonds       : bond        0.03811 (  263)
  hydrogen bonds       : angle       5.31123 (  699)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  677 MET cc_start: 0.8152 (mmt) cc_final: 0.7797 (mmt)
REVERT: A 1040 ASP cc_start: 0.8550 (t0) cc_final: 0.8252 (t0)
REVERT: B  172 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7650 (tt0)
  outliers start: 16
  outliers final: 9
  residues processed: 97
  average time/residue: 0.0634
  time to fit residues: 9.3097
Evaluate side-chains
  92 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  718 HIS
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  770 GLU
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue 1246 PHE
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.0970
   chunk 43 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 89 optimal weight:    8.9990
   chunk 3 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0980
   chunk 36 optimal weight:    6.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1093 GLN
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 103 HIS
B 328 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.113426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.100874 restraints weight = 18857.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.103440 restraints weight = 9792.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.105145 restraints weight = 6118.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.106320 restraints weight = 4232.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.107070 restraints weight = 3180.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8780  Z= 0.143
  Angle     :  0.603   6.253  11905  Z= 0.310
  Chirality :  0.045   0.145   1350
  Planarity :  0.004   0.050   1515
  Dihedral  :  4.704  21.370   1173
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 18.53 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.26), residues: 1067
  helix:  0.08 (0.34), residues: 262
  sheet:  0.06 (0.37), residues: 216
  loop : -2.10 (0.26), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 621 
 TYR   0.013   0.001   TYR A 575 
 PHE   0.019   0.002   PHE A 704 
 TRP   0.018   0.002   TRP A 900 
 HIS   0.005   0.001   HIS A 663 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8780)
  covalent geometry    : angle       0.60291 (11905)
  hydrogen bonds       : bond        0.04661 (  263)
  hydrogen bonds       : angle       5.23091 (  699)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A  677 MET cc_start: 0.8210 (mmt) cc_final: 0.7782 (mmt)
REVERT: A 1040 ASP cc_start: 0.8541 (t0) cc_final: 0.8204 (t0)
REVERT: A 1229 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7313 (tmm)
REVERT: B  172 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7838 (tt0)
  outliers start: 21
  outliers final: 11
  residues processed: 97
  average time/residue: 0.0721
  time to fit residues: 10.8384
Evaluate side-chains
  92 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0370
   chunk 53 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0270
   chunk 18 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 105 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.9920

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

Flipped N/Q/H residues before XYZ refinement:
** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.113743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.101246 restraints weight = 18780.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.103859 restraints weight = 9757.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.105573 restraints weight = 5999.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.106643 restraints weight = 4171.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.107510 restraints weight = 3184.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8780  Z= 0.124
  Angle     :  0.586   6.899  11905  Z= 0.298
  Chirality :  0.044   0.142   1350
  Planarity :  0.004   0.050   1515
  Dihedral  :  4.617  21.722   1173
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 20.11 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.26), residues: 1067
  helix:  0.02 (0.34), residues: 264
  sheet: -0.23 (0.36), residues: 225
  loop : -2.11 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 621 
 TYR   0.012   0.001   TYR A 575 
 PHE   0.019   0.001   PHE A 704 
 TRP   0.020   0.001   TRP A 900 
 HIS   0.003   0.001   HIS A 663 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8780)
  covalent geometry    : angle       0.58615 (11905)
  hydrogen bonds       : bond        0.04249 (  263)
  hydrogen bonds       : angle       5.16059 (  699)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  677 MET cc_start: 0.8152 (mmt) cc_final: 0.7698 (mmt)
REVERT: A 1040 ASP cc_start: 0.8534 (t0) cc_final: 0.8203 (t0)
REVERT: A 1229 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7279 (tmm)
  outliers start: 19
  outliers final: 14
  residues processed: 99
  average time/residue: 0.0648
  time to fit residues: 9.9925
Evaluate side-chains
  95 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1246 PHE
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 66 optimal weight:    0.2980
   chunk 73 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1093 GLN
A1178 HIS
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.115198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.102818 restraints weight = 18572.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.105456 restraints weight = 9576.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.107190 restraints weight = 5861.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.108369 restraints weight = 4030.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.109153 restraints weight = 3009.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8780  Z= 0.106
  Angle     :  0.574   9.348  11905  Z= 0.290
  Chirality :  0.044   0.140   1350
  Planarity :  0.004   0.049   1515
  Dihedral  :  4.500  21.696   1173
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 21.16 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.26), residues: 1067
  helix:  0.11 (0.34), residues: 264
  sheet: -0.19 (0.36), residues: 224
  loop : -2.05 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 621 
 TYR   0.013   0.001   TYR A 575 
 PHE   0.018   0.001   PHE A 704 
 TRP   0.023   0.001   TRP A 900 
 HIS   0.002   0.001   HIS A 663 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 8780)
  covalent geometry    : angle       0.57428 (11905)
  hydrogen bonds       : bond        0.03777 (  263)
  hydrogen bonds       : angle       5.04385 (  699)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  677 MET cc_start: 0.8153 (mmt) cc_final: 0.7648 (mmt)
REVERT: A  885 ASP cc_start: 0.6609 (m-30) cc_final: 0.6123 (m-30)
REVERT: A 1040 ASP cc_start: 0.8532 (t0) cc_final: 0.8153 (t0)
REVERT: A 1229 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7283 (tmm)
  outliers start: 18
  outliers final: 15
  residues processed: 99
  average time/residue: 0.0677
  time to fit residues: 10.3102
Evaluate side-chains
  97 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1178 HIS
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1246 PHE
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 42 optimal weight:    0.5980
   chunk 90 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 96 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.114846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.102407 restraints weight = 18780.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.105027 restraints weight = 9726.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.106757 restraints weight = 5950.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.107919 restraints weight = 4099.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.108741 restraints weight = 3073.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8780  Z= 0.114
  Angle     :  0.583   8.205  11905  Z= 0.295
  Chirality :  0.043   0.141   1350
  Planarity :  0.004   0.049   1515
  Dihedral  :  4.501  21.412   1173
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 21.05 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.26), residues: 1067
  helix:  0.06 (0.34), residues: 269
  sheet:  0.04 (0.37), residues: 214
  loop : -2.19 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 621 
 TYR   0.010   0.001   TYR A 575 
 PHE   0.018   0.001   PHE A 704 
 TRP   0.024   0.001   TRP A 900 
 HIS   0.003   0.001   HIS A1178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8780)
  covalent geometry    : angle       0.58342 (11905)
  hydrogen bonds       : bond        0.03927 (  263)
  hydrogen bonds       : angle       4.98274 (  699)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  677 MET cc_start: 0.8158 (mmt) cc_final: 0.7632 (mmt)
REVERT: A  885 ASP cc_start: 0.6650 (m-30) cc_final: 0.6168 (m-30)
REVERT: A 1040 ASP cc_start: 0.8532 (t0) cc_final: 0.8134 (t0)
REVERT: A 1229 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7294 (tmm)
  outliers start: 24
  outliers final: 16
  residues processed: 99
  average time/residue: 0.0648
  time to fit residues: 10.0312
Evaluate side-chains
  97 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1246 PHE
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 106 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0670
   chunk 73 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   overall best weight:    1.7724

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

Flipped N/Q/H residues before XYZ refinement:
** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1090 GLN
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.110659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.098291 restraints weight = 18813.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.100827 restraints weight = 9803.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.102504 restraints weight = 6073.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.103649 restraints weight = 4226.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.104361 restraints weight = 3183.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8780  Z= 0.188
  Angle     :  0.664  10.483  11905  Z= 0.339
  Chirality :  0.046   0.228   1350
  Planarity :  0.005   0.050   1515
  Dihedral  :  4.859  21.851   1173
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 21.89 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.84 (0.26), residues: 1067
  helix: -0.06 (0.33), residues: 268
  sheet: -0.34 (0.36), residues: 223
  loop : -2.25 (0.25), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 621 
 TYR   0.014   0.002   TYR A 575 
 PHE   0.020   0.002   PHE A 704 
 TRP   0.025   0.002   TRP A 900 
 HIS   0.005   0.001   HIS A 663 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 8780)
  covalent geometry    : angle       0.66385 (11905)
  hydrogen bonds       : bond        0.05464 (  263)
  hydrogen bonds       : angle       5.31433 (  699)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  718 HIS cc_start: 0.7182 (OUTLIER) cc_final: 0.6973 (m-70)
REVERT: A 1040 ASP cc_start: 0.8542 (t0) cc_final: 0.8163 (t0)
REVERT: A 1178 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7122 (t-90)
REVERT: A 1229 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7299 (tmm)
  outliers start: 27
  outliers final: 14
  residues processed: 102
  average time/residue: 0.0733
  time to fit residues: 11.4187
Evaluate side-chains
  96 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  718 HIS
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1178 HIS
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0570
   chunk 2 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
A1093 GLN
A1178 HIS
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.106855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.093949 restraints weight = 19302.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.096492 restraints weight = 10171.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.098208 restraints weight = 6308.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.099314 restraints weight = 4385.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.100178 restraints weight = 3346.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8780  Z= 0.111
  Angle     :  0.610   8.750  11905  Z= 0.305
  Chirality :  0.044   0.143   1350
  Planarity :  0.004   0.049   1515
  Dihedral  :  4.609  22.859   1173
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 22.63 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.26), residues: 1067
  helix: -0.04 (0.33), residues: 276
  sheet: -0.06 (0.37), residues: 213
  loop : -2.28 (0.25), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 621 
 TYR   0.014   0.001   TYR A 575 
 PHE   0.018   0.001   PHE A 704 
 TRP   0.031   0.001   TRP A 900 
 HIS   0.003   0.001   HIS A 663 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8780)
  covalent geometry    : angle       0.60972 (11905)
  hydrogen bonds       : bond        0.04010 (  263)
  hydrogen bonds       : angle       5.11938 (  699)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A  661 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7309 (tm-30)
REVERT: A  677 MET cc_start: 0.8252 (mmt) cc_final: 0.7776 (mmt)
REVERT: A  845 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8705 (tt)
REVERT: A  885 ASP cc_start: 0.6801 (m-30) cc_final: 0.6281 (m-30)
REVERT: A 1040 ASP cc_start: 0.8517 (t0) cc_final: 0.8108 (t0)
REVERT: A 1229 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7317 (tmm)
  outliers start: 21
  outliers final: 16
  residues processed: 101
  average time/residue: 0.0680
  time to fit residues: 10.3580
Evaluate side-chains
  102 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  635 LYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1178 HIS
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 105 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 96 optimal weight:    0.0970
   chunk 19 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.107004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.094072 restraints weight = 19170.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.096620 restraints weight = 10097.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.098340 restraints weight = 6276.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.099427 restraints weight = 4369.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.100295 restraints weight = 3343.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8780  Z= 0.113
  Angle     :  0.620  10.290  11905  Z= 0.310
  Chirality :  0.044   0.141   1350
  Planarity :  0.005   0.084   1515
  Dihedral  :  4.545  21.546   1173
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 22.21 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.26), residues: 1067
  helix: -0.00 (0.33), residues: 276
  sheet: -0.10 (0.37), residues: 217
  loop : -2.21 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 621 
 TYR   0.012   0.001   TYR A 575 
 PHE   0.018   0.001   PHE A 704 
 TRP   0.031   0.001   TRP A 900 
 HIS   0.003   0.001   HIS A 928 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8780)
  covalent geometry    : angle       0.62006 (11905)
  hydrogen bonds       : bond        0.03966 (  263)
  hydrogen bonds       : angle       5.04908 (  699)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  661 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7327 (tm-30)
REVERT: A  677 MET cc_start: 0.8292 (mmt) cc_final: 0.7822 (mmt)
REVERT: A  718 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.7101 (m-70)
REVERT: A  845 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8719 (tt)
REVERT: A  885 ASP cc_start: 0.6797 (m-30) cc_final: 0.6273 (m-30)
REVERT: A 1040 ASP cc_start: 0.8546 (t0) cc_final: 0.8134 (t0)
REVERT: A 1178 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.7102 (t-90)
REVERT: A 1229 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7304 (tmm)
  outliers start: 24
  outliers final: 18
  residues processed: 104
  average time/residue: 0.0663
  time to fit residues: 10.4931
Evaluate side-chains
  105 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  595 SER
Chi-restraints excluded: chain A residue  635 LYS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  718 HIS
Chi-restraints excluded: chain A residue  727 THR
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  910 ILE
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1178 HIS
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1269 GLU
Chi-restraints excluded: chain A residue 1271 CYS
Chi-restraints excluded: chain B residue  103 HIS
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  402 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 12 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 39 optimal weight:    7.9990
   chunk 84 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0060
   chunk 91 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.108524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.095499 restraints weight = 19187.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.098073 restraints weight = 10116.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.099835 restraints weight = 6286.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.101000 restraints weight = 4367.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.101863 restraints weight = 3310.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8780  Z= 0.105
  Angle     :  0.612   9.779  11905  Z= 0.303
  Chirality :  0.044   0.141   1350
  Planarity :  0.004   0.073   1515
  Dihedral  :  4.433  21.826   1173
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 22.95 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.49 (0.27), residues: 1067
  helix:  0.14 (0.34), residues: 264
  sheet:  0.08 (0.37), residues: 213
  loop : -2.01 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 621 
 TYR   0.014   0.001   TYR A 575 
 PHE   0.018   0.001   PHE A 704 
 TRP   0.033   0.001   TRP A 900 
 HIS   0.003   0.001   HIS A 928 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 8780)
  covalent geometry    : angle       0.61193 (11905)
  hydrogen bonds       : bond        0.03515 (  263)
  hydrogen bonds       : angle       4.96777 (  699)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1431.83 seconds
wall clock time: 25 minutes 24.01 seconds (1524.01 seconds total)