Starting phenix.real_space_refine
on Sat Aug 23 04:54:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bwp_16293/08_2025/8bwp_16293.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bwp_16293/08_2025/8bwp_16293.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bwp_16293/08_2025/8bwp_16293.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bwp_16293/08_2025/8bwp_16293.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bwp_16293/08_2025/8bwp_16293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bwp_16293/08_2025/8bwp_16293.map"
  }
  resolution = 3.6
  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=   0.070
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    6221      2.51       5
     N    1610      2.21       5
     O    1704      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9578
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1195, 9545
          Classifications: {'peptide': 1195}
          Link IDs: {'PTRANS': 37, 'TRANS': 1157}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 33
          Unusual residues: {'MTX': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.41, per 1000 atoms: 0.25
  Number of scatterers: 9578
  At special positions: 0
  Unit cell: (77.376, 107.328, 144.768, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1704      8.00
     N    1610      7.00
     C    6221      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: 1.02
  Conformation dependent library (CDL) restraints added in 309.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue is complicated and confusing
        pdb=" CB  MTX A1401 "
  Number of C-beta restraints generated:  2266

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 5 sheets defined
      73.1% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 15
    Processing helix  chain 'A' and resid 17 through 22
    Processing helix  chain 'A' and resid 24 through 26
      No H-bonds generated for 'chain 'A' and resid 24 through 26'
    Processing helix  chain 'A' and resid 27 through 35
      removed outlier: 3.742A  pdb=" N   PHE A  31 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 75
      removed outlier: 4.316A  pdb=" N   GLY A  62 " --> pdb=" O   GLU A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 87
      removed outlier: 3.769A  pdb=" N   ALA A  83 " --> pdb=" O   SER A  79 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ILE A  85 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 121
      removed outlier: 4.157A  pdb=" N   LEU A  93 " --> pdb=" O   TRP A  89 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   VAL A  94 " --> pdb=" O   LYS A  90 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   LEU A  95 " --> pdb=" O   SER A  91 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLY A  96 " --> pdb=" O   TYR A  92 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE A  98 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE A 101 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LYS A 106 " --> pdb=" O   GLU A 102 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
      removed outlier: 3.578A  pdb=" N   PHE A 120 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 150
    Processing helix  chain 'A' and resid 150 through 181
      removed outlier: 3.956A  pdb=" N   LEU A 154 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLY A 163 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU A 166 " --> pdb=" O   ALA A 162 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ARG A 180 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 189
    Processing helix  chain 'A' and resid 190 through 200
    Processing helix  chain 'A' and resid 201 through 203
      No H-bonds generated for 'chain 'A' and resid 201 through 203'
    Processing helix  chain 'A' and resid 204 through 212
      removed outlier: 4.337A  pdb=" N   THR A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   VAL A 210 " --> pdb=" O   ASP A 206 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   PHE A 211 " --> pdb=" O   GLN A 207 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU A 212 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 233
      Proline residue:  A 219  - end of helix
    Processing helix  chain 'A' and resid 235 through 246
      removed outlier: 3.944A  pdb=" N   ALA A 239 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 282
      removed outlier: 3.893A  pdb=" N   LEU A 250 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   THR A 267 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   PHE A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 289
    Processing helix  chain 'A' and resid 291 through 342
      removed outlier: 4.369A  pdb=" N   LYS A 309 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   ARG A 312 " --> pdb=" O   SER A 308 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   SER A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   LYS A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 367
      removed outlier: 3.690A  pdb=" N   ALA A 354 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   LEU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   THR A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 391
      removed outlier: 3.509A  pdb=" N   LEU A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 460
    Processing helix  chain 'A' and resid 489 through 495
    Processing helix  chain 'A' and resid 500 through 511
    Processing helix  chain 'A' and resid 513 through 521
    Processing helix  chain 'A' and resid 529 through 533
    Processing helix  chain 'A' and resid 536 through 551
      removed outlier: 3.534A  pdb=" N   LEU A 545 " --> pdb=" O   ALA A 541 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLN A 551 " --> pdb=" O   ARG A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 576
      removed outlier: 4.392A  pdb=" N   PHE A 574 " --> pdb=" O   SER A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 600
      removed outlier: 3.873A  pdb=" N   LYS A 598 " --> pdb=" O   GLN A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 620
    Processing helix  chain 'A' and resid 697 through 709
      removed outlier: 3.505A  pdb=" N   GLY A 708 " --> pdb=" O   TYR A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 745
      removed outlier: 3.647A  pdb=" N   PHE A 714 " --> pdb=" O   HIS A 710 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASP A 732 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 808
      removed outlier: 3.708A  pdb=" N   GLY A 766 " --> pdb=" O   ASN A 762 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLU A 803 " --> pdb=" O   ASN A 799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 816
      removed outlier: 3.697A  pdb=" N   PHE A 813 " --> pdb=" O   PRO A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 827
      removed outlier: 3.636A  pdb=" N   ARG A 824 " --> pdb=" O   ARG A 820 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   PHE A 825 " --> pdb=" O   ILE A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 835
      removed outlier: 4.611A  pdb=" N   ASP A 833 " --> pdb=" O   ILE A 829 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 861
    Processing helix  chain 'A' and resid 864 through 896
      Proline residue:  A 870  - end of helix
      removed outlier: 3.599A  pdb=" N   ARG A 880 " --> pdb=" O   ILE A 876 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   THR A 885 " --> pdb=" O   TYR A 881 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   ASP A 888 " --> pdb=" O   GLU A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 897 through 909
      removed outlier: 3.891A  pdb=" N   PHE A 901 " --> pdb=" O   ARG A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 910 through 917
      removed outlier: 3.724A  pdb=" N   TYR A 917 " --> pdb=" O   THR A 913 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 919 through 970
      removed outlier: 4.016A  pdb=" N   CYS A 923 " --> pdb=" O   ALA A 919 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   PHE A 927 " --> pdb=" O   CYS A 923 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LEU A 933 " --> pdb=" O   ALA A 929 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLU A 936 " --> pdb=" O   ASP A 932 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   SER A 945 " --> pdb=" O   PHE A 941 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   CYS A 956 " --> pdb=" O   LEU A 952 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 968 " --> pdb=" O   ALA A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 987
    Processing helix  chain 'A' and resid 988 through 1007
      removed outlier: 3.524A  pdb=" N   MET A 992 " --> pdb=" O   THR A 988 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   GLN A 994 " --> pdb=" O   MET A 990 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TRP A 995 " --> pdb=" O   GLY A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1007 through 1018
      removed outlier: 3.772A  pdb=" N   TYR A1016 " --> pdb=" O   ARG A1012 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASP A1018 " --> pdb=" O   ILE A1014 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1082 through 1089
    Processing helix  chain 'A' and resid 1109 through 1116
      removed outlier: 3.689A  pdb=" N   LYS A1115 " --> pdb=" O   HIS A1111 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LYS A1116 " --> pdb=" O   ASP A1112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1130 through 1136
    Processing helix  chain 'A' and resid 1142 through 1153
    Processing helix  chain 'A' and resid 1155 through 1161
    Processing helix  chain 'A' and resid 1164 through 1168
    Processing helix  chain 'A' and resid 1171 through 1175
    Processing helix  chain 'A' and resid 1178 through 1194
    Processing helix  chain 'A' and resid 1203 through 1207
    Processing helix  chain 'A' and resid 1208 through 1223
    Processing helix  chain 'A' and resid 1234 through 1238
    Processing helix  chain 'A' and resid 1257 through 1264
    Processing helix  chain 'A' and resid 1267 through 1275
    Processing helix  chain 'A' and resid 1276 through 1278
      No H-bonds generated for 'chain 'A' and resid 1276 through 1278'
    Processing helix  chain 'A' and resid 1279 through 1294
    Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435
      removed outlier: 5.804A  pdb=" N   GLN A 429 " --> pdb=" O   ALA A 417 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   ALA A 417 " --> pdb=" O   GLN A 429 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   PHE A 433 " --> pdb=" O   GLN A 413 " (cutoff:3.500A)
      removed outlier: 4.851A  pdb=" N   GLN A 413 " --> pdb=" O   PHE A 433 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   VAL A 435 " --> pdb=" O   HIS A 411 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   HIS A 411 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   PHE A 415 " --> pdb=" O   HIS A 466 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   HIS A 466 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478
      removed outlier: 6.847A  pdb=" N   ALA A 476 " --> pdb=" O   LEU A 557 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ALA A 442 " --> pdb=" O   LEU A 604 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   LEU A 606 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   VAL A 444 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   LYS A 607 " --> pdb=" O   MET A 611 " (cutoff:3.500A)
      removed outlier: 5.186A  pdb=" N   MET A 611 " --> pdb=" O   LYS A 607 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488
      removed outlier: 4.644A  pdb=" N   GLY A 487 " --> pdb=" O   ILE A 528 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1058 through 1065
      removed outlier: 5.790A  pdb=" N   LYS A1059 " --> pdb=" O   PHE A1048 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   PHE A1048 " --> pdb=" O   LYS A1059 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   ALA A1063 " --> pdb=" O   ASP A1044 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   ASP A1044 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   ILE A1065 " --> pdb=" O   ILE A1042 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   ILE A1042 " --> pdb=" O   ILE A1065 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   VAL A1046 " --> pdb=" O   GLU A1095 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   GLU A1095 " --> pdb=" O   VAL A1046 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1117 through 1120
      removed outlier: 6.451A  pdb=" N   LEU A1198 " --> pdb=" O   LEU A1229 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   ILE A1231 " --> pdb=" O   LEU A1198 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   ILE A1200 " --> pdb=" O   ILE A1231 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   LYS A1070 " --> pdb=" O   LYS A1243 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   MET A1245 " --> pdb=" O   LYS A1070 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   GLY A1072 " --> pdb=" O   MET A1245 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   LEU A1247 " --> pdb=" O   GLY A1072 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   VAL A1074 " --> pdb=" O   LEU A1247 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ILE A1244 " --> pdb=" O   TYR A1255 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   TYR A1255 " --> pdb=" O   ILE A1244 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   VAL A1246 " --> pdb=" O   LYS A1253 " (cutoff:3.500A)

    609 hydrogen bonds defined for protein.
    1761 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: 1.80

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3024
        1.34 -     1.46: 1607
        1.46 -     1.58: 5082
        1.58 -     1.69: 1
        1.69 -     1.81: 70
  Bond restraints: 9784
  Sorted by residual:
  bond pdb=" C2  MTX A1401 "
       pdb=" NA2 MTX A1401 "
    ideal  model  delta    sigma   weight residual
    1.341  1.407 -0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" CG  LEU A  27 "
       pdb=" CD1 LEU A  27 "
    ideal  model  delta    sigma   weight residual
    1.521  1.440  0.081 3.30e-02 9.18e+02 5.97e+00
  bond pdb=" CB  GLN A 931 "
       pdb=" CG  GLN A 931 "
    ideal  model  delta    sigma   weight residual
    1.520  1.452  0.068 3.00e-02 1.11e+03 5.12e+00
  bond pdb=" C8A MTX A1401 "
       pdb=" N8  MTX A1401 "
    ideal  model  delta    sigma   weight residual
    1.348  1.393 -0.045 2.00e-02 2.50e+03 5.09e+00
  bond pdb=" CB  ARG A 946 "
       pdb=" CG  ARG A 946 "
    ideal  model  delta    sigma   weight residual
    1.520  1.452  0.068 3.00e-02 1.11e+03 5.09e+00
  ... (remaining 9779 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 12676
        1.88 -     3.77: 488
        3.77 -     5.65: 75
        5.65 -     7.54: 18
        7.54 -     9.42: 5
  Bond angle restraints: 13262
  Sorted by residual:
  angle pdb=" C   THR A 943 "
        pdb=" N   THR A 944 "
        pdb=" CA  THR A 944 "
      ideal   model   delta    sigma   weight residual
     120.29  115.76    4.53 1.42e+00 4.96e-01 1.02e+01
  angle pdb=" CB  ARG A 951 "
        pdb=" CG  ARG A 951 "
        pdb=" CD  ARG A 951 "
      ideal   model   delta    sigma   weight residual
     111.30  118.25   -6.95 2.30e+00 1.89e-01 9.12e+00
  angle pdb=" CA  GLN A 849 "
        pdb=" CB  GLN A 849 "
        pdb=" CG  GLN A 849 "
      ideal   model   delta    sigma   weight residual
     114.10  120.10   -6.00 2.00e+00 2.50e-01 9.00e+00
  angle pdb=" C   HIS A 153 "
        pdb=" N   LEU A 154 "
        pdb=" CA  LEU A 154 "
      ideal   model   delta    sigma   weight residual
     120.29  116.07    4.22 1.42e+00 4.96e-01 8.84e+00
  angle pdb=" CA  ARG A 951 "
        pdb=" CB  ARG A 951 "
        pdb=" CG  ARG A 951 "
      ideal   model   delta    sigma   weight residual
     114.10  119.50   -5.40 2.00e+00 2.50e-01 7.30e+00
  ... (remaining 13257 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.96: 5411
       16.96 -    33.92: 329
       33.92 -    50.87: 71
       50.87 -    67.83: 17
       67.83 -    84.79: 7
  Dihedral angle restraints: 5835
    sinusoidal: 2341
      harmonic: 3494
  Sorted by residual:
  dihedral pdb=" CA  LEU A1091 "
           pdb=" C   LEU A1091 "
           pdb=" N   SER A1092 "
           pdb=" CA  SER A1092 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.13   25.87     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  CYS A1226 "
           pdb=" C   CYS A1226 "
           pdb=" N   THR A1227 "
           pdb=" CA  THR A1227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.45   24.55     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  LYS A1021 "
           pdb=" C   LYS A1021 "
           pdb=" N   GLU A1022 "
           pdb=" CA  GLU A1022 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.39   23.61     0      5.00e+00 4.00e-02 2.23e+01
  ... (remaining 5832 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1187
       0.068 -    0.136: 309
       0.136 -    0.204: 38
       0.204 -    0.272: 3
       0.272 -    0.340: 1
  Chirality restraints: 1538
  Sorted by residual:
  chirality pdb=" CA  MTX A1401 "
            pdb=" N   MTX A1401 "
            pdb=" CB  MTX A1401 "
            pdb=" CT  MTX A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.25   -0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" CA  PHE A 258 "
            pdb=" N   PHE A 258 "
            pdb=" C   PHE A 258 "
            pdb=" CB  PHE A 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CA  PHE A  24 "
            pdb=" N   PHE A  24 "
            pdb=" C   PHE A  24 "
            pdb=" CB  PHE A  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1535 not shown)

  Planarity restraints: 1646
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  26 "   -0.020 2.00e-02 2.50e+03   1.55e-02 5.98e+00
        pdb=" CG  TRP A  26 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  26 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  26 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  26 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  26 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  26 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  26 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  26 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  26 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 939 "   -0.024 2.00e-02 2.50e+03   1.84e-02 5.91e+00
        pdb=" CG  PHE A 939 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 939 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 939 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 939 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 939 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 939 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1292 "    0.009 2.00e-02 2.50e+03   1.64e-02 5.40e+00
        pdb=" CG  TYR A1292 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1292 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1292 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1292 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1292 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1292 "   -0.022 2.00e-02 2.50e+03
        pdb=" OH  TYR A1292 "    0.027 2.00e-02 2.50e+03
  ... (remaining 1643 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1421
        2.75 -     3.29: 10324
        3.29 -     3.83: 15536
        3.83 -     4.36: 18837
        4.36 -     4.90: 31944
  Nonbonded interactions: 78062
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 303 "
            pdb=" OE1 GLU A 306 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OH  TYR A  92 "
            pdb=" O   THR A 209 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   SER A1241 "
            pdb=" OH  TYR A1292 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   GLU A 521 "
            pdb=" OG1 THR A 526 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OG1 THR A 269 "
            pdb=" OE2 GLU A 306 "
     model   vdw
     2.247 3.040
  ... (remaining 78057 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             4.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.980
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:   17.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
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      :  0.011   0.081   9784  Z= 0.457
  Angle     :  0.899   9.422  13262  Z= 0.492
  Chirality :  0.060   0.340   1538
  Planarity :  0.008   0.078   1646
  Dihedral  : 12.537  84.791   3569
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  1.82 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.09 %
  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 aren not related in a simple way.
  whole: -1.51 (0.22), residues: 1187
  helix: -1.44 (0.15), residues: 769
  sheet:  0.56 (0.78), residues: 50
  loop :  0.32 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.003   ARG A 897 
 TYR   0.028   0.005   TYR A 881 
 PHE   0.042   0.004   PHE A 939 
 TRP   0.042   0.003   TRP A  26 
 HIS   0.014   0.002   HIS A 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.01091 ( 9784)
  covalent geometry    : angle       0.89889 (13262)
  hydrogen bonds       : bond        0.22442 (  609)
  hydrogen bonds       : angle       8.61477 ( 1761)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 207
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASP cc_start: 0.8467 (t0) cc_final: 0.8211 (t0)
REVERT: A   67 GLU cc_start: 0.8510 (tp30) cc_final: 0.8278 (tp30)
REVERT: A  200 ASN cc_start: 0.8411 (t0) cc_final: 0.7787 (t0)
REVERT: A  206 ASP cc_start: 0.7918 (t70) cc_final: 0.7708 (t70)
REVERT: A  276 MET cc_start: 0.8329 (tpp) cc_final: 0.8109 (tpp)
REVERT: A  316 LEU cc_start: 0.8398 (tp) cc_final: 0.7992 (tt)
REVERT: A  728 TYR cc_start: 0.8546 (t80) cc_final: 0.8310 (t80)
REVERT: A  953 ASP cc_start: 0.8492 (m-30) cc_final: 0.7945 (m-30)
REVERT: A  985 TYR cc_start: 0.8166 (m-80) cc_final: 0.7717 (m-80)
REVERT: A  998 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.7020 (mmt-90)
REVERT: A 1045 ASN cc_start: 0.9065 (t0) cc_final: 0.8806 (t0)
REVERT: A 1104 LEU cc_start: 0.9073 (tp) cc_final: 0.8539 (tp)
REVERT: A 1122 GLN cc_start: 0.7517 (tt0) cc_final: 0.6847 (tm-30)
REVERT: A 1136 ASP cc_start: 0.7587 (t0) cc_final: 0.6875 (t0)
REVERT: A 1196 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7622 (mp10)
REVERT: A 1212 ASP cc_start: 0.8769 (t0) cc_final: 0.8279 (m-30)
REVERT: A 1253 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8766 (mmtm)
  outliers start: 5
  outliers final: 3
  residues processed: 211
  average time/residue: 0.1314
  time to fit residues: 36.7520
Evaluate side-chains
  140 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 137
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  485 PHE
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue 1230 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.200689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.158718 restraints weight = 11588.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.157692 restraints weight = 13697.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.158529 restraints weight = 12300.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.159743 restraints weight = 7193.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.160156 restraints weight = 5829.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9784  Z= 0.163
  Angle     :  0.611   8.259  13262  Z= 0.330
  Chirality :  0.043   0.178   1538
  Planarity :  0.004   0.041   1646
  Dihedral  :  6.766  82.755   1304
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  8.06 %
    Favored  : 90.02 %
  Cbeta Deviations :  0.09 %
  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 aren not related in a simple way.
  whole:  0.39 (0.24), residues: 1187
  helix:  0.27 (0.18), residues: 788
  sheet:  0.50 (0.76), residues: 52
  loop :  0.60 (0.37), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1220 
 TYR   0.024   0.002   TYR A1292 
 PHE   0.034   0.002   PHE A 258 
 TRP   0.012   0.001   TRP A 711 
 HIS   0.005   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9784)
  covalent geometry    : angle       0.61135 (13262)
  hydrogen bonds       : bond        0.05262 (  609)
  hydrogen bonds       : angle       4.99194 ( 1761)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 184
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  706 ARG cc_start: 0.7865 (tpp-160) cc_final: 0.7528 (mmt180)
REVERT: A  744 MET cc_start: 0.7258 (mmm) cc_final: 0.6826 (mtp)
REVERT: A  990 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7422 (ptp)
REVERT: A 1016 TYR cc_start: 0.7783 (m-10) cc_final: 0.6667 (m-10)
REVERT: A 1136 ASP cc_start: 0.7759 (t0) cc_final: 0.7170 (t70)
  outliers start: 20
  outliers final: 14
  residues processed: 195
  average time/residue: 0.1097
  time to fit residues: 30.0172
Evaluate side-chains
  155 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 TRP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  183 ASN
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 PHE
Chi-restraints excluded: chain A residue  710 HIS
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  990 MET
Chi-restraints excluded: chain A residue 1049 MET
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1230 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 110 optimal weight:    4.9990
   chunk 113 optimal weight:    0.6980
   chunk 45 optimal weight:   10.0000
   chunk 111 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 95 optimal weight:    8.9990
   chunk 74 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A1134 ASN
A1206 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.199546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.157928 restraints weight = 11486.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.156429 restraints weight = 14760.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.158193 restraints weight = 13740.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.158776 restraints weight = 7711.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.160000 restraints weight = 6738.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9784  Z= 0.172
  Angle     :  0.586   7.724  13262  Z= 0.312
  Chirality :  0.042   0.177   1538
  Planarity :  0.004   0.034   1646
  Dihedral  :  6.495  86.844   1303
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 11.23 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.09 %
  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 aren not related in a simple way.
  whole:  0.78 (0.25), residues: 1187
  helix:  0.59 (0.18), residues: 785
  sheet:  1.21 (0.83), residues: 47
  loop :  0.62 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1030 
 TYR   0.023   0.002   TYR A 289 
 PHE   0.032   0.002   PHE A 258 
 TRP   0.011   0.001   TRP A 947 
 HIS   0.004   0.001   HIS A 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 9784)
  covalent geometry    : angle       0.58588 (13262)
  hydrogen bonds       : bond        0.04761 (  609)
  hydrogen bonds       : angle       4.70252 ( 1761)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 154
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 GLN cc_start: 0.8624 (tp40) cc_final: 0.8299 (tp40)
REVERT: A   67 GLU cc_start: 0.8683 (tp30) cc_final: 0.8379 (tp30)
REVERT: A  289 TYR cc_start: 0.7983 (m-80) cc_final: 0.7781 (m-80)
REVERT: A  706 ARG cc_start: 0.7928 (tpp-160) cc_final: 0.7539 (mmt180)
REVERT: A  744 MET cc_start: 0.7245 (mmm) cc_final: 0.6741 (mtp)
REVERT: A 1016 TYR cc_start: 0.7659 (m-10) cc_final: 0.6683 (m-10)
REVERT: A 1122 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7723 (tp40)
REVERT: A 1136 ASP cc_start: 0.7908 (t0) cc_final: 0.7361 (t0)
REVERT: A 1146 LEU cc_start: 0.8549 (mt) cc_final: 0.8318 (tt)
  outliers start: 32
  outliers final: 26
  residues processed: 178
  average time/residue: 0.1006
  time to fit residues: 25.5383
Evaluate side-chains
  162 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   25 TRP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 PHE
Chi-restraints excluded: chain A residue  710 HIS
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  883 LEU
Chi-restraints excluded: chain A residue  895 THR
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue 1049 MET
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1082 SER
Chi-restraints excluded: chain A residue 1118 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A1068 GLN
A1134 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.200186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.159461 restraints weight = 11535.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.160182 restraints weight = 13230.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.161062 restraints weight = 11315.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.161530 restraints weight = 6894.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.162156 restraints weight = 5901.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9784  Z= 0.159
  Angle     :  0.567   7.485  13262  Z= 0.300
  Chirality :  0.042   0.172   1538
  Planarity :  0.004   0.033   1646
  Dihedral  :  6.349  88.853   1302
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 11.80 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.09 %
  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 aren not related in a simple way.
  whole:  0.95 (0.25), residues: 1187
  helix:  0.73 (0.18), residues: 787
  sheet:  1.37 (0.85), residues: 47
  loop :  0.63 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1030 
 TYR   0.018   0.002   TYR A 289 
 PHE   0.034   0.002   PHE A 258 
 TRP   0.013   0.001   TRP A1025 
 HIS   0.004   0.001   HIS A1225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 9784)
  covalent geometry    : angle       0.56740 (13262)
  hydrogen bonds       : bond        0.04359 (  609)
  hydrogen bonds       : angle       4.50217 ( 1761)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 148
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 GLN cc_start: 0.8657 (tp40) cc_final: 0.8151 (tp-100)
REVERT: A  241 MET cc_start: 0.7799 (mmm) cc_final: 0.7488 (mmm)
REVERT: A  706 ARG cc_start: 0.7864 (tpp-160) cc_final: 0.7484 (mmt180)
REVERT: A  744 MET cc_start: 0.7293 (mmm) cc_final: 0.6923 (mtt)
REVERT: A  904 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8122 (tp)
REVERT: A 1016 TYR cc_start: 0.7644 (m-10) cc_final: 0.6759 (m-10)
REVERT: A 1122 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7800 (tp40)
REVERT: A 1136 ASP cc_start: 0.7972 (t0) cc_final: 0.7432 (t0)
  outliers start: 34
  outliers final: 23
  residues processed: 170
  average time/residue: 0.1068
  time to fit residues: 25.5813
Evaluate side-chains
  164 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   25 TRP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 PHE
Chi-restraints excluded: chain A residue  710 HIS
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  895 THR
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue 1005 ASN
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1082 SER
Chi-restraints excluded: chain A residue 1125 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 112 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0980
   chunk 21 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0370
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A1134 ASN
** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.201823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.160301 restraints weight = 11484.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.159623 restraints weight = 14324.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.161301 restraints weight = 13679.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.161850 restraints weight = 7690.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.165015 restraints weight = 6400.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9784  Z= 0.136
  Angle     :  0.547   9.776  13262  Z= 0.285
  Chirality :  0.041   0.171   1538
  Planarity :  0.003   0.033   1646
  Dihedral  :  6.136  86.566   1302
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 13.34 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.09 %
  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 aren not related in a simple way.
  whole:  1.15 (0.25), residues: 1187
  helix:  0.90 (0.19), residues: 789
  sheet:  1.48 (0.85), residues: 47
  loop :  0.64 (0.36), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1030 
 TYR   0.026   0.001   TYR A 289 
 PHE   0.033   0.002   PHE A 258 
 TRP   0.011   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 934 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9784)
  covalent geometry    : angle       0.54652 (13262)
  hydrogen bonds       : bond        0.04142 (  609)
  hydrogen bonds       : angle       4.39359 ( 1761)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 143
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 GLN cc_start: 0.8596 (tp40) cc_final: 0.8111 (tp-100)
REVERT: A  276 MET cc_start: 0.7832 (mmm) cc_final: 0.7525 (mmm)
REVERT: A  289 TYR cc_start: 0.7949 (m-80) cc_final: 0.7703 (m-80)
REVERT: A  706 ARG cc_start: 0.7824 (tpp-160) cc_final: 0.7421 (mmt180)
REVERT: A  744 MET cc_start: 0.7063 (mmm) cc_final: 0.6787 (mtt)
REVERT: A  904 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8124 (tp)
REVERT: A 1016 TYR cc_start: 0.7662 (m-10) cc_final: 0.6819 (m-10)
REVERT: A 1122 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7427 (tp40)
REVERT: A 1136 ASP cc_start: 0.7894 (t0) cc_final: 0.7539 (t0)
  outliers start: 29
  outliers final: 25
  residues processed: 163
  average time/residue: 0.1061
  time to fit residues: 24.3961
Evaluate side-chains
  159 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   25 TRP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 PHE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  710 HIS
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1082 SER
Chi-restraints excluded: chain A residue 1118 SER
Chi-restraints excluded: chain A residue 1125 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 33 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 116 optimal weight:    9.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.201116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.160128 restraints weight = 11472.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.160324 restraints weight = 13798.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.161280 restraints weight = 11355.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.161976 restraints weight = 6654.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.162448 restraints weight = 5748.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.3753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9784  Z= 0.149
  Angle     :  0.558   9.120  13262  Z= 0.292
  Chirality :  0.041   0.176   1538
  Planarity :  0.004   0.042   1646
  Dihedral  :  5.968  82.216   1302
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 13.92 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.09 %
  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 aren not related in a simple way.
  whole:  1.22 (0.25), residues: 1187
  helix:  0.95 (0.19), residues: 789
  sheet:  1.40 (0.84), residues: 47
  loop :  0.69 (0.36), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1030 
 TYR   0.028   0.001   TYR A 289 
 PHE   0.033   0.002   PHE A 258 
 TRP   0.013   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 934 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9784)
  covalent geometry    : angle       0.55756 (13262)
  hydrogen bonds       : bond        0.04076 (  609)
  hydrogen bonds       : angle       4.38449 ( 1761)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 GLN cc_start: 0.8585 (tp40) cc_final: 0.8060 (tp-100)
REVERT: A  276 MET cc_start: 0.7738 (mmm) cc_final: 0.7501 (mmm)
REVERT: A  706 ARG cc_start: 0.7775 (tpp-160) cc_final: 0.7390 (mmt180)
REVERT: A  744 MET cc_start: 0.7059 (mmm) cc_final: 0.6821 (mtt)
REVERT: A  904 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8129 (tp)
REVERT: A 1016 TYR cc_start: 0.7673 (m-10) cc_final: 0.6851 (m-10)
REVERT: A 1120 ILE cc_start: 0.8928 (mp) cc_final: 0.8665 (pt)
REVERT: A 1122 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7977 (tp40)
REVERT: A 1136 ASP cc_start: 0.7942 (t0) cc_final: 0.7595 (t0)
  outliers start: 29
  outliers final: 23
  residues processed: 157
  average time/residue: 0.1044
  time to fit residues: 23.2657
Evaluate side-chains
  155 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   25 TRP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 PHE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  710 HIS
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  895 THR
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue 1005 ASN
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1125 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 87 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 89 optimal weight:    0.0970
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.5578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.202684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.161380 restraints weight = 11403.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.159776 restraints weight = 12650.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.161511 restraints weight = 11804.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.161940 restraints weight = 6747.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.162616 restraints weight = 5717.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9784  Z= 0.133
  Angle     :  0.550   9.077  13262  Z= 0.286
  Chirality :  0.041   0.231   1538
  Planarity :  0.004   0.036   1646
  Dihedral  :  5.749  76.717   1302
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 14.59 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.09 %
  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 aren not related in a simple way.
  whole:  1.32 (0.25), residues: 1187
  helix:  1.02 (0.19), residues: 791
  sheet:  1.41 (0.83), residues: 47
  loop :  0.77 (0.36), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1030 
 TYR   0.030   0.001   TYR A 289 
 PHE   0.034   0.002   PHE A 258 
 TRP   0.011   0.001   TRP A1099 
 HIS   0.003   0.001   HIS A 934 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9784)
  covalent geometry    : angle       0.55033 (13262)
  hydrogen bonds       : bond        0.03935 (  609)
  hydrogen bonds       : angle       4.31902 ( 1761)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 138
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 GLN cc_start: 0.8602 (tp40) cc_final: 0.8056 (tp-100)
REVERT: A  706 ARG cc_start: 0.7809 (tpp-160) cc_final: 0.7411 (mmt180)
REVERT: A  744 MET cc_start: 0.7170 (mmm) cc_final: 0.6888 (mtt)
REVERT: A  904 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8045 (tp)
REVERT: A 1016 TYR cc_start: 0.7609 (m-10) cc_final: 0.6822 (m-10)
REVERT: A 1120 ILE cc_start: 0.8861 (mp) cc_final: 0.8594 (pt)
REVERT: A 1136 ASP cc_start: 0.7992 (t0) cc_final: 0.7265 (p0)
  outliers start: 30
  outliers final: 25
  residues processed: 160
  average time/residue: 0.0999
  time to fit residues: 22.9808
Evaluate side-chains
  156 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   25 TRP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  485 PHE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  710 HIS
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  904 LEU
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1005 ASN
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1082 SER
Chi-restraints excluded: chain A residue 1272 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 93 optimal weight:    0.0070
   chunk 84 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0040
   chunk 61 optimal weight:    2.9990
   chunk 16 optimal weight:    0.3980
   chunk 45 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 59 optimal weight:    0.2980
   chunk 39 optimal weight:    3.9990
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.2610

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.206013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.164549 restraints weight = 11292.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.164378 restraints weight = 13920.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.165620 restraints weight = 12760.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.166282 restraints weight = 7542.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.166978 restraints weight = 6620.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.4135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9784  Z= 0.116
  Angle     :  0.543   9.756  13262  Z= 0.280
  Chirality :  0.041   0.313   1538
  Planarity :  0.003   0.037   1646
  Dihedral  :  5.489  68.883   1302
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.74 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.09 %
  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 aren not related in a simple way.
  whole:  1.51 (0.25), residues: 1187
  helix:  1.17 (0.19), residues: 794
  sheet:  1.38 (0.70), residues: 58
  loop :  0.82 (0.37), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1030 
 TYR   0.028   0.001   TYR A 289 
 PHE   0.034   0.001   PHE A 324 
 TRP   0.012   0.001   TRP A1099 
 HIS   0.003   0.001   HIS A 934 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9784)
  covalent geometry    : angle       0.54311 (13262)
  hydrogen bonds       : bond        0.03743 (  609)
  hydrogen bonds       : angle       4.22171 ( 1761)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.8969 (tp) cc_final: 0.8752 (tp)
REVERT: A   61 GLN cc_start: 0.8582 (tp40) cc_final: 0.8020 (tp-100)
REVERT: A  706 ARG cc_start: 0.7816 (tpp-160) cc_final: 0.7442 (mmt180)
REVERT: A  744 MET cc_start: 0.7383 (mmm) cc_final: 0.7004 (mtt)
REVERT: A 1016 TYR cc_start: 0.7526 (m-10) cc_final: 0.6786 (m-80)
REVERT: A 1136 ASP cc_start: 0.7756 (t0) cc_final: 0.7356 (p0)
  outliers start: 24
  outliers final: 20
  residues processed: 157
  average time/residue: 0.1016
  time to fit residues: 22.9367
Evaluate side-chains
  148 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  485 PHE
Chi-restraints excluded: chain A residue  710 HIS
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue 1005 ASN
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1169 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.200448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.159540 restraints weight = 11475.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.157647 restraints weight = 15629.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.158828 restraints weight = 14393.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.160319 restraints weight = 7723.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.160880 restraints weight = 6108.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.4154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9784  Z= 0.157
  Angle     :  0.594   9.951  13262  Z= 0.303
  Chirality :  0.043   0.271   1538
  Planarity :  0.004   0.036   1646
  Dihedral  :  5.430  64.394   1302
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.93 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.09 %
  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 aren not related in a simple way.
  whole:  1.46 (0.25), residues: 1187
  helix:  1.12 (0.19), residues: 785
  sheet:  1.36 (0.69), residues: 58
  loop :  0.84 (0.37), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1030 
 TYR   0.031   0.002   TYR A1259 
 PHE   0.033   0.002   PHE A 258 
 TRP   0.012   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A1111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 9784)
  covalent geometry    : angle       0.59370 (13262)
  hydrogen bonds       : bond        0.04053 (  609)
  hydrogen bonds       : angle       4.30705 ( 1761)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 139
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 GLN cc_start: 0.8593 (tp40) cc_final: 0.8116 (tp-100)
REVERT: A  289 TYR cc_start: 0.8165 (m-80) cc_final: 0.7950 (m-80)
REVERT: A  706 ARG cc_start: 0.7807 (tpp-160) cc_final: 0.7504 (mmt180)
REVERT: A  744 MET cc_start: 0.7024 (mmm) cc_final: 0.6808 (mtt)
REVERT: A 1016 TYR cc_start: 0.7596 (m-10) cc_final: 0.6878 (m-80)
REVERT: A 1136 ASP cc_start: 0.7642 (t0) cc_final: 0.7227 (p0)
REVERT: A 1143 ASP cc_start: 0.8115 (t0) cc_final: 0.7713 (t0)
REVERT: A 1245 MET cc_start: 0.7777 (mmm) cc_final: 0.7552 (mmm)
  outliers start: 29
  outliers final: 27
  residues processed: 157
  average time/residue: 0.0960
  time to fit residues: 21.6696
Evaluate side-chains
  161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  485 PHE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  710 HIS
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  895 THR
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1005 ASN
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1082 SER
Chi-restraints excluded: chain A residue 1169 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   chunk 112 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 59 optimal weight:    4.9990
   chunk 114 optimal weight:   10.0000
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.198034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.157490 restraints weight = 11382.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.153813 restraints weight = 13716.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.155904 restraints weight = 15128.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.156336 restraints weight = 8438.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.157020 restraints weight = 7314.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.4124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9784  Z= 0.217
  Angle     :  0.660  10.125  13262  Z= 0.337
  Chirality :  0.044   0.262   1538
  Planarity :  0.004   0.034   1646
  Dihedral  :  5.577  63.391   1302
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.31 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.09 %
  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 aren not related in a simple way.
  whole:  1.19 (0.25), residues: 1187
  helix:  0.93 (0.19), residues: 782
  sheet:  1.45 (0.70), residues: 58
  loop :  0.65 (0.36), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1030 
 TYR   0.027   0.002   TYR A 477 
 PHE   0.032   0.002   PHE A 258 
 TRP   0.013   0.001   TRP A 947 
 HIS   0.005   0.001   HIS A 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 9784)
  covalent geometry    : angle       0.66019 (13262)
  hydrogen bonds       : bond        0.04405 (  609)
  hydrogen bonds       : angle       4.46912 ( 1761)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 139
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 GLN cc_start: 0.8612 (tp40) cc_final: 0.8125 (tp-100)
REVERT: A  289 TYR cc_start: 0.8272 (m-80) cc_final: 0.7926 (m-80)
REVERT: A  706 ARG cc_start: 0.7847 (tpp-160) cc_final: 0.7521 (mmt180)
REVERT: A 1016 TYR cc_start: 0.7690 (m-10) cc_final: 0.6928 (m-80)
REVERT: A 1136 ASP cc_start: 0.7532 (t0) cc_final: 0.7157 (p0)
  outliers start: 31
  outliers final: 28
  residues processed: 161
  average time/residue: 0.1038
  time to fit residues: 23.8885
Evaluate side-chains
  160 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   25 TRP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  485 PHE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  710 HIS
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain A residue  895 THR
Chi-restraints excluded: chain A residue  902 SER
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1005 ASN
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1082 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 117 optimal weight:    7.9990
   chunk 82 optimal weight:    0.1980
   chunk 105 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 903 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.222272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.178814 restraints weight = 11875.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.176016 restraints weight = 8942.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.177338 restraints weight = 9794.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.178236 restraints weight = 5756.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.178731 restraints weight = 4996.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.4338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9784  Z= 0.145
  Angle     :  0.597   9.601  13262  Z= 0.303
  Chirality :  0.042   0.225   1538
  Planarity :  0.004   0.035   1646
  Dihedral  :  5.465  57.740   1302
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.99 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.09 %
  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 aren not related in a simple way.
  whole:  1.36 (0.25), residues: 1187
  helix:  1.05 (0.19), residues: 783
  sheet:  1.48 (0.70), residues: 58
  loop :  0.73 (0.37), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1030 
 TYR   0.038   0.002   TYR A 550 
 PHE   0.033   0.001   PHE A 258 
 TRP   0.013   0.001   TRP A1099 
 HIS   0.003   0.001   HIS A 934 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 9784)
  covalent geometry    : angle       0.59653 (13262)
  hydrogen bonds       : bond        0.04025 (  609)
  hydrogen bonds       : angle       4.29438 ( 1761)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1647.00 seconds
wall clock time: 29 minutes 24.28 seconds (1764.28 seconds total)