Starting phenix.real_space_refine
on Wed Sep 17 17:34:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qfp_13946/09_2025/7qfp_13946.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qfp_13946/09_2025/7qfp_13946.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qfp_13946/09_2025/7qfp_13946.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qfp_13946/09_2025/7qfp_13946.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qfp_13946/09_2025/7qfp_13946.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qfp_13946/09_2025/7qfp_13946.map"
  }
  resolution = 3.7
  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=  -0.002 sd=   0.026
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      23      5.16       5
     C    6363      2.51       5
     N    1670      2.21       5
     O    1940      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9996
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1233, 9996
          Classifications: {'peptide': 1233}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 33, 'TRANS': 1199}
          Chain breaks: 1
  Time building chain proxies: 2.21, per 1000 atoms: 0.22
  Number of scatterers: 9996
  At special positions: 0
  Unit cell: (94.6, 99.76, 122.98, 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      23     16.00
     O    1940      8.00
     N    1670      7.00
     C    6363      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 429 " - pdb=" SG  CYS A 443 " distance=2.04

  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: 1.01
  Conformation dependent library (CDL) restraints added in 394.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2352

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 18 sheets defined
      26.4% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 111
      removed outlier: 3.941A  pdb=" N   LEU A 101 " --> pdb=" O   LYS A  97 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   LYS A 106 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE A 111 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 126
      removed outlier: 3.606A  pdb=" N   LYS A 126 " --> pdb=" O   GLU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 188
      removed outlier: 3.779A  pdb=" N   ASN A 187 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 238
      removed outlier: 3.794A  pdb=" N   THR A 226 " --> pdb=" O   ASP A 222 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLN A 230 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 273
      removed outlier: 3.509A  pdb=" N   LEU A 270 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 305
      removed outlier: 3.977A  pdb=" N   TYR A 289 " --> pdb=" O   SER A 285 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   LYS A 305 " --> pdb=" O   SER A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
      removed outlier: 3.696A  pdb=" N   LYS A 317 " --> pdb=" O   ASN A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 323
    Processing helix  chain 'A' and resid 337 through 349
      removed outlier: 3.613A  pdb=" N   PHE A 341 " --> pdb=" O   ASN A 337 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LYS A 346 " --> pdb=" O   ASN A 342 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   TYR A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 360
      removed outlier: 3.721A  pdb=" N   LEU A 356 " --> pdb=" O   THR A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 399
      removed outlier: 3.658A  pdb=" N   VAL A 399 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 544
      removed outlier: 3.898A  pdb=" N   TYR A 539 " --> pdb=" O   ASN A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 581
    Processing helix  chain 'A' and resid 585 through 587
      No H-bonds generated for 'chain 'A' and resid 585 through 587'
    Processing helix  chain 'A' and resid 588 through 605
      removed outlier: 4.952A  pdb=" N   GLN A 594 " --> pdb=" O   VAL A 590 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASN A 605 " --> pdb=" O   THR A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 646
      removed outlier: 4.643A  pdb=" N   ALA A 641 " --> pdb=" O   ASN A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 710
      removed outlier: 3.836A  pdb=" N   VAL A 680 " --> pdb=" O   ASN A 676 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL A 698 " --> pdb=" O   LYS A 694 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   TYR A 699 " --> pdb=" O   TRP A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 729
      removed outlier: 3.762A  pdb=" N   PHE A 714 " --> pdb=" O   ILE A 710 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLU A 719 " --> pdb=" O   ASN A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 742
    Processing helix  chain 'A' and resid 760 through 817
      removed outlier: 4.624A  pdb=" N   ASN A 773 " --> pdb=" O   SER A 769 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   ASN A 774 " --> pdb=" O   ILE A 770 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ILE A 775 " --> pdb=" O   ALA A 771 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   SER A 783 " --> pdb=" O   LEU A 779 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE A 784 " --> pdb=" O   THR A 780 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLU A 793 " --> pdb=" O   LYS A 789 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE A 796 " --> pdb=" O   ASN A 792 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASN A 797 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   LYS A 798 " --> pdb=" O   VAL A 794 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   LEU A 799 " --> pdb=" O   LYS A 795 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ARG A 800 " --> pdb=" O   ILE A 796 " (cutoff:3.500A)
      removed outlier: 5.645A  pdb=" N   GLU A 801 " --> pdb=" O   ASN A 797 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 836
    Processing helix  chain 'A' and resid 945 through 949
    Processing helix  chain 'A' and resid 1072 through 1083
      removed outlier: 3.510A  pdb=" N   ILE A1076 " --> pdb=" O   ASP A1072 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLN A1077 " --> pdb=" O   GLU A1073 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   THR A1078 " --> pdb=" O   THR A1074 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU A1079 " --> pdb=" O   GLU A1075 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TYR A1080 " --> pdb=" O   ILE A1076 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN A1082 " --> pdb=" O   THR A1078 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1172 through 1176
      removed outlier: 3.853A  pdb=" N   LEU A1176 " --> pdb=" O   LYS A1173 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38
      removed outlier: 6.729A  pdb=" N   TRP A  57 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL A 201 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 85
      removed outlier: 3.662A  pdb=" N   VAL A 422 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150
    Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 211
    Processing sheet with id=AA5, first strand: chain 'A' and resid 249 through 250
      removed outlier: 3.531A  pdb=" N   ILE A 250 " --> pdb=" O   THR A 264 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   THR A 264 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 327 through 328
    Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 377
    Processing sheet with id=AA8, first strand: chain 'A' and resid 872 through 873
    Processing sheet with id=AA9, first strand: chain 'A' and resid 889 through 891
    Processing sheet with id=AB1, first strand: chain 'A' and resid 905 through 906
      removed outlier: 3.565A  pdb=" N   PHE A 905 " --> pdb=" O   ILE A1061 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1008 through 1012
      removed outlier: 3.602A  pdb=" N   ILE A 934 " --> pdb=" O   ILE A1012 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 990 through 993
      removed outlier: 3.781A  pdb=" N   PHE A 992 " --> pdb=" O   ILE A 976 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE A 976 " --> pdb=" O   PHE A 992 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLU A 975 " --> pdb=" O   ASN A 972 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LYS A 968 " --> pdb=" O   THR A 979 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLN A 981 " --> pdb=" O   GLY A 966 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   TRP A 967 " --> pdb=" O   ASN A 958 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   ASN A 958 " --> pdb=" O   TRP A 967 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   VAL A 969 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   TYR A 954 " --> pdb=" O   LEU A 971 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   TYR A 954 " --> pdb=" O   VAL A1051 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   VAL A1051 " --> pdb=" O   TYR A 954 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ILE A 956 " --> pdb=" O   LYS A1049 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1019 through 1024
      removed outlier: 6.474A  pdb=" N   SER A1020 " --> pdb=" O   GLN A1031 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   GLN A1031 " --> pdb=" O   SER A1020 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LEU A1022 " --> pdb=" O   ILE A1029 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ILE A1029 " --> pdb=" O   LEU A1022 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1104 through 1107
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1113 through 1117
      removed outlier: 3.600A  pdb=" N   ASN A1127 " --> pdb=" O   PHE A1114 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   ASP A1116 " --> pdb=" O   ILE A1125 " (cutoff:3.500A)
      removed outlier: 5.106A  pdb=" N   ILE A1125 " --> pdb=" O   ASP A1116 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1168 through 1169
      removed outlier: 3.506A  pdb=" N   PHE A1177 " --> pdb=" O   PHE A1169 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1204 through 1209
      removed outlier: 3.533A  pdb=" N   LYS A1219 " --> pdb=" O   VAL A1204 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   PHE A1218 " --> pdb=" O   ILE A1226 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1228 through 1229

    248 hydrogen bonds defined for protein.
    678 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: 1.85

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2831
        1.33 -     1.46: 2025
        1.46 -     1.58: 5299
        1.58 -     1.70: 0
        1.70 -     1.83: 38
  Bond restraints: 10193
  Sorted by residual:
  bond pdb=" C   VAL A 545 "
       pdb=" N   PRO A 546 "
    ideal  model  delta    sigma   weight residual
    1.332  1.398 -0.066 1.30e-02 5.92e+03 2.58e+01
  bond pdb=" N   PRO A 941 "
       pdb=" CA  PRO A 941 "
    ideal  model  delta    sigma   weight residual
    1.469  1.523 -0.054 1.28e-02 6.10e+03 1.80e+01
  bond pdb=" N   PRO A 498 "
       pdb=" CA  PRO A 498 "
    ideal  model  delta    sigma   weight residual
    1.479  1.541 -0.062 1.56e-02 4.11e+03 1.57e+01
  bond pdb=" N   VAL A1204 "
       pdb=" CA  VAL A1204 "
    ideal  model  delta    sigma   weight residual
    1.455  1.496 -0.041 1.18e-02 7.18e+03 1.21e+01
  bond pdb=" N   ILE A 509 "
       pdb=" CA  ILE A 509 "
    ideal  model  delta    sigma   weight residual
    1.459  1.501 -0.042 1.25e-02 6.40e+03 1.14e+01
  ... (remaining 10188 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 12717
        2.03 -     4.06: 968
        4.06 -     6.09: 93
        6.09 -     8.12: 21
        8.12 -    10.15: 11
  Bond angle restraints: 13810
  Sorted by residual:
  angle pdb=" C   VAL A 545 "
        pdb=" N   PRO A 546 "
        pdb=" CA  PRO A 546 "
      ideal   model   delta    sigma   weight residual
     119.76  127.20   -7.44 1.03e+00 9.43e-01 5.22e+01
  angle pdb=" C   ILE A 940 "
        pdb=" N   PRO A 941 "
        pdb=" CA  PRO A 941 "
      ideal   model   delta    sigma   weight residual
     119.84  128.85   -9.01 1.25e+00 6.40e-01 5.20e+01
  angle pdb=" N   ASN A 964 "
        pdb=" CA  ASN A 964 "
        pdb=" C   ASN A 964 "
      ideal   model   delta    sigma   weight residual
     113.23  106.16    7.07 1.22e+00 6.72e-01 3.35e+01
  angle pdb=" N   ILE A 864 "
        pdb=" CA  ILE A 864 "
        pdb=" C   ILE A 864 "
      ideal   model   delta    sigma   weight residual
     110.53  115.93   -5.40 9.40e-01 1.13e+00 3.30e+01
  angle pdb=" N   ASP A 484 "
        pdb=" CA  ASP A 484 "
        pdb=" C   ASP A 484 "
      ideal   model   delta    sigma   weight residual
     113.18  106.42    6.76 1.21e+00 6.83e-01 3.12e+01
  ... (remaining 13805 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 5298
       16.92 -    33.85: 637
       33.85 -    50.77: 156
       50.77 -    67.69: 31
       67.69 -    84.61: 11
  Dihedral angle restraints: 6133
    sinusoidal: 2483
      harmonic: 3650
  Sorted by residual:
  dihedral pdb=" CB  CYS A 429 "
           pdb=" SG  CYS A 429 "
           pdb=" SG  CYS A 443 "
           pdb=" CB  CYS A 443 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.43   72.43     1      1.00e+01 1.00e-02 6.70e+01
  dihedral pdb=" C   ASN A 265 "
           pdb=" N   ASN A 265 "
           pdb=" CA  ASN A 265 "
           pdb=" CB  ASN A 265 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.43   11.83     0      2.50e+00 1.60e-01 2.24e+01
  dihedral pdb=" C   ASP A 486 "
           pdb=" N   ASP A 486 "
           pdb=" CA  ASP A 486 "
           pdb=" CB  ASP A 486 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.28   11.68     0      2.50e+00 1.60e-01 2.18e+01
  ... (remaining 6130 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1120
       0.074 -    0.149: 298
       0.149 -    0.223: 84
       0.223 -    0.297: 25
       0.297 -    0.371: 9
  Chirality restraints: 1536
  Sorted by residual:
  chirality pdb=" CA  ASN A 265 "
            pdb=" N   ASN A 265 "
            pdb=" C   ASN A 265 "
            pdb=" CB  ASN A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.45e+00
  chirality pdb=" CA  ASP A 486 "
            pdb=" N   ASP A 486 "
            pdb=" C   ASP A 486 "
            pdb=" CB  ASP A 486 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.28e+00
  chirality pdb=" CA  ASP A 944 "
            pdb=" N   ASP A 944 "
            pdb=" C   ASP A 944 "
            pdb=" CB  ASP A 944 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.26e+00
  ... (remaining 1533 not shown)

  Planarity restraints: 1793
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 391 "    0.018 2.00e-02 2.50e+03   3.58e-02 1.28e+01
        pdb=" C   GLY A 391 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   GLY A 391 "    0.023 2.00e-02 2.50e+03
        pdb=" N   TYR A 392 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 171 "    0.049 5.00e-02 4.00e+02   7.39e-02 8.74e+00
        pdb=" N   PRO A 172 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO A 172 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 172 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 314 "    0.047 5.00e-02 4.00e+02   7.20e-02 8.29e+00
        pdb=" N   PRO A 315 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO A 315 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 315 "    0.041 5.00e-02 4.00e+02
  ... (remaining 1790 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 539
        2.71 -     3.26: 10159
        3.26 -     3.81: 16402
        3.81 -     4.35: 19915
        4.35 -     4.90: 31467
  Nonbonded interactions: 78482
  Sorted by model distance:
  nonbonded pdb=" N   GLU A 267 "
            pdb=" OE1 GLU A 267 "
     model   vdw
     2.167 3.120
  nonbonded pdb=" O   ARG A 419 "
            pdb=" NH1 ARG A 419 "
     model   vdw
     2.186 3.120
  nonbonded pdb=" N   GLN A 371 "
            pdb=" OE1 GLN A 371 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" O   ASN A  27 "
            pdb=" ND2 ASN A  27 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" O   ALA A 604 "
            pdb=" OH  TYR A 622 "
     model   vdw
     2.288 3.040
  ... (remaining 78477 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.660
  Find NCS groups from input model:        0.050
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
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      :  0.007   0.066  10194  Z= 0.472
  Angle     :  1.110  10.154  13812  Z= 0.746
  Chirality :  0.081   0.371   1536
  Planarity :  0.006   0.074   1793
  Dihedral  : 15.770  84.612   3778
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 19.15
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  : 12.53 %
    Favored  : 86.90 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 12.86 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.34 %
  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: -4.48 (0.19), residues: 1229
  helix: -2.54 (0.21), residues: 333
  sheet: -2.82 (0.47), residues: 98
  loop : -3.41 (0.18), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 863 
 TYR   0.021   0.002   TYR A 233 
 PHE   0.012   0.001   PHE A 905 
 TRP   0.009   0.001   TRP A 937 
 HIS   0.004   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00653 (10193)
  covalent geometry    : angle       1.10904 (13810)
  SS BOND              : bond        0.01246 (    1)
  SS BOND              : angle       3.32848 (    2)
  hydrogen bonds       : bond        0.21323 (  248)
  hydrogen bonds       : angle       7.86305 (  678)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 211
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  268 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7718 (mm-30)
REVERT: A  503 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7834 (pm20)
REVERT: A  578 ASN cc_start: 0.9012 (m110) cc_final: 0.8457 (p0)
REVERT: A  637 ASN cc_start: 0.7768 (p0) cc_final: 0.7499 (p0)
REVERT: A  645 LEU cc_start: 0.7880 (mt) cc_final: 0.7609 (mt)
REVERT: A  689 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8564 (pttt)
REVERT: A  693 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7907 (mt-10)
REVERT: A  758 LYS cc_start: 0.4694 (OUTLIER) cc_final: 0.4485 (pttm)
REVERT: A  870 LEU cc_start: 0.8615 (tp) cc_final: 0.8402 (tt)
REVERT: A 1044 ASP cc_start: 0.9154 (p0) cc_final: 0.8867 (p0)
REVERT: A 1076 ILE cc_start: 0.8187 (mm) cc_final: 0.7916 (mm)
REVERT: A 1101 LYS cc_start: 0.5580 (OUTLIER) cc_final: 0.5375 (mmmt)
REVERT: A 1114 PHE cc_start: 0.7803 (t80) cc_final: 0.7430 (t80)
REVERT: A 1163 ASP cc_start: 0.7158 (t0) cc_final: 0.6799 (t0)
REVERT: A 1201 PHE cc_start: 0.8283 (m-80) cc_final: 0.7551 (m-80)
  outliers start: 47
  outliers final: 15
  residues processed: 252
  average time/residue: 0.1070
  time to fit residues: 37.5296
Evaluate side-chains
  145 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  324 TYR
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  447 ASN
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  757 ILE
Chi-restraints excluded: chain A residue  758 LYS
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  930 LYS
Chi-restraints excluded: chain A residue 1040 ILE
Chi-restraints excluded: chain A residue 1098 LEU
Chi-restraints excluded: chain A residue 1101 LYS
Chi-restraints excluded: chain A residue 1186 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 117 optimal weight:    8.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
A 214 ASN
A 286 ASN
A 291 ASN
** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 342 ASN
A 382 ASN
A 400 ASN
A 407 ASN
A 448 ASN
A 634 GLN
A 685 ASN
** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 727 ASN
A 765 ASN
A 805 ASN
A 837 ASN
A 871 ASN
A 945 ASN
A 983 ASN
A1025 ASN
** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1203 GLN
A1224 ASN
A1251 ASN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.106414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.083935 restraints weight = 35937.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.086507 restraints weight = 20090.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.088233 restraints weight = 13835.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.089465 restraints weight = 10722.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.090276 restraints weight = 9016.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10194  Z= 0.180
  Angle     :  0.691   7.654  13812  Z= 0.370
  Chirality :  0.047   0.162   1536
  Planarity :  0.005   0.068   1793
  Dihedral  :  7.409  73.752   1377
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.39 %
    Favored  : 88.53 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 18.59 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.81 (0.21), residues: 1229
  helix: -1.10 (0.27), residues: 329
  sheet: -2.61 (0.42), residues: 120
  loop : -3.39 (0.19), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 873 
 TYR   0.021   0.002   TYR A1023 
 PHE   0.028   0.002   PHE A 670 
 TRP   0.015   0.001   TRP A1241 
 HIS   0.002   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (10193)
  covalent geometry    : angle       0.69041 (13810)
  SS BOND              : bond        0.00617 (    1)
  SS BOND              : angle       2.55813 (    2)
  hydrogen bonds       : bond        0.04230 (  248)
  hydrogen bonds       : angle       5.39814 (  678)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 127
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6239 (mmm) cc_final: 0.5798 (mmm)
REVERT: A  123 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8348 (tm-30)
REVERT: A  578 ASN cc_start: 0.9015 (m110) cc_final: 0.8331 (p0)
REVERT: A  600 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8628 (m-80)
REVERT: A  637 ASN cc_start: 0.7609 (p0) cc_final: 0.7355 (p0)
REVERT: A  645 LEU cc_start: 0.8014 (mt) cc_final: 0.7710 (mt)
REVERT: A  758 LYS cc_start: 0.4530 (OUTLIER) cc_final: 0.4043 (pttm)
REVERT: A 1044 ASP cc_start: 0.9199 (p0) cc_final: 0.8974 (p0)
REVERT: A 1163 ASP cc_start: 0.7169 (t0) cc_final: 0.6807 (t0)
REVERT: A 1201 PHE cc_start: 0.8825 (m-80) cc_final: 0.8435 (m-80)
  outliers start: 51
  outliers final: 21
  residues processed: 161
  average time/residue: 0.0960
  time to fit residues: 22.4277
Evaluate side-chains
  131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  443 CYS
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  727 ASN
Chi-restraints excluded: chain A residue  758 LYS
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  857 PHE
Chi-restraints excluded: chain A residue  889 ILE
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue 1040 ILE
Chi-restraints excluded: chain A residue 1042 VAL
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1098 LEU
Chi-restraints excluded: chain A residue 1138 LEU
Chi-restraints excluded: chain A residue 1237 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 114 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   chunk 103 optimal weight:    0.0270
   overall best weight:    1.4842

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
A 407 ASN
A 510 GLN
** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 727 ASN
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.106385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.083907 restraints weight = 36344.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.086482 restraints weight = 20541.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.088195 restraints weight = 14221.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.089387 restraints weight = 11096.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.090003 restraints weight = 9336.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10194  Z= 0.139
  Angle     :  0.664  17.193  13812  Z= 0.347
  Chirality :  0.046   0.157   1536
  Planarity :  0.004   0.058   1793
  Dihedral  :  6.496  80.701   1348
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.96 %
    Favored  : 87.96 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 20.18 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -3.40 (0.22), residues: 1229
  helix: -0.51 (0.29), residues: 329
  sheet: -2.31 (0.43), residues: 118
  loop : -3.25 (0.19), residues: 782

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 863 
 TYR   0.018   0.001   TYR A1023 
 PHE   0.018   0.001   PHE A 211 
 TRP   0.007   0.001   TRP A 978 
 HIS   0.001   0.001   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10193)
  covalent geometry    : angle       0.65905 (13810)
  SS BOND              : bond        0.00875 (    1)
  SS BOND              : angle       7.05769 (    2)
  hydrogen bonds       : bond        0.03877 (  248)
  hydrogen bonds       : angle       5.02759 (  678)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 122
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6270 (mmm) cc_final: 0.5840 (mmm)
REVERT: A  123 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8382 (tm-30)
REVERT: A  158 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7728 (mm110)
REVERT: A  460 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.6375 (m-80)
REVERT: A  544 LYS cc_start: 0.8997 (mmtm) cc_final: 0.8771 (mmtp)
REVERT: A  578 ASN cc_start: 0.9030 (m110) cc_final: 0.8364 (p0)
REVERT: A  600 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8608 (m-80)
REVERT: A  637 ASN cc_start: 0.7695 (p0) cc_final: 0.7450 (p0)
REVERT: A  645 LEU cc_start: 0.8003 (mt) cc_final: 0.7647 (mt)
REVERT: A  758 LYS cc_start: 0.4566 (OUTLIER) cc_final: 0.4237 (pttm)
REVERT: A  872 MET cc_start: 0.8425 (tmm) cc_final: 0.8206 (tmm)
REVERT: A  930 LYS cc_start: 0.7764 (tppt) cc_final: 0.7504 (tppt)
REVERT: A 1044 ASP cc_start: 0.9173 (p0) cc_final: 0.8932 (p0)
REVERT: A 1063 TYR cc_start: 0.7299 (m-80) cc_final: 0.7071 (m-80)
REVERT: A 1070 GLU cc_start: 0.4549 (tp30) cc_final: 0.4083 (tp30)
REVERT: A 1163 ASP cc_start: 0.7215 (t0) cc_final: 0.6862 (t0)
REVERT: A 1201 PHE cc_start: 0.8788 (m-80) cc_final: 0.8286 (m-80)
  outliers start: 44
  outliers final: 21
  residues processed: 152
  average time/residue: 0.0949
  time to fit residues: 21.1765
Evaluate side-chains
  131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  458 ASN
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  514 TYR
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  727 ASN
Chi-restraints excluded: chain A residue  758 LYS
Chi-restraints excluded: chain A residue  889 ILE
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue 1042 VAL
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1125 ILE
Chi-restraints excluded: chain A residue 1138 LEU
Chi-restraints excluded: chain A residue 1237 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 115 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 80 optimal weight:    9.9990
   chunk 112 optimal weight:    6.9990
   chunk 73 optimal weight:    4.9990
   chunk 41 optimal weight:    0.4980
   chunk 36 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 88 optimal weight:    9.9990
   chunk 111 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1041 HIS
** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.104360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.081834 restraints weight = 36663.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.084283 restraints weight = 20661.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.086000 restraints weight = 14357.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.087175 restraints weight = 11236.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.087955 restraints weight = 9472.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.3737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10194  Z= 0.159
  Angle     :  0.647  12.266  13812  Z= 0.339
  Chirality :  0.045   0.157   1536
  Planarity :  0.004   0.060   1793
  Dihedral  :  6.287  82.276   1342
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 12.37 %
    Favored  : 87.55 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.41 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -3.30 (0.22), residues: 1229
  helix: -0.37 (0.29), residues: 341
  sheet: -2.23 (0.45), residues: 111
  loop : -3.26 (0.20), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 863 
 TYR   0.023   0.001   TYR A1180 
 PHE   0.016   0.002   PHE A 211 
 TRP   0.018   0.001   TRP A1241 
 HIS   0.002   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (10193)
  covalent geometry    : angle       0.64625 (13810)
  SS BOND              : bond        0.02892 (    1)
  SS BOND              : angle       2.85204 (    2)
  hydrogen bonds       : bond        0.03883 (  248)
  hydrogen bonds       : angle       4.91475 (  678)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 113
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6357 (mmm) cc_final: 0.5885 (mmm)
REVERT: A  123 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8453 (tm-30)
REVERT: A  460 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.6452 (m-80)
REVERT: A  544 LYS cc_start: 0.9023 (mmtm) cc_final: 0.8788 (mmtp)
REVERT: A  578 ASN cc_start: 0.9017 (m110) cc_final: 0.8815 (m110)
REVERT: A  600 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8618 (m-80)
REVERT: A  637 ASN cc_start: 0.7702 (p0) cc_final: 0.7455 (p0)
REVERT: A  645 LEU cc_start: 0.7847 (mt) cc_final: 0.7574 (mt)
REVERT: A  758 LYS cc_start: 0.4618 (OUTLIER) cc_final: 0.4387 (pttm)
REVERT: A  872 MET cc_start: 0.8297 (tmm) cc_final: 0.8074 (tmm)
REVERT: A 1044 ASP cc_start: 0.9198 (p0) cc_final: 0.8983 (p0)
REVERT: A 1070 GLU cc_start: 0.4436 (tp30) cc_final: 0.4090 (tp30)
REVERT: A 1163 ASP cc_start: 0.7365 (t0) cc_final: 0.7025 (t0)
REVERT: A 1180 TYR cc_start: 0.8472 (t80) cc_final: 0.8102 (t80)
REVERT: A 1201 PHE cc_start: 0.8752 (m-80) cc_final: 0.8459 (m-80)
  outliers start: 44
  outliers final: 27
  residues processed: 142
  average time/residue: 0.1015
  time to fit residues: 20.7951
Evaluate side-chains
  132 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  126 LYS
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  458 ASN
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  514 TYR
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  727 ASN
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  758 LYS
Chi-restraints excluded: chain A residue  932 PHE
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue 1042 VAL
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1125 ILE
Chi-restraints excluded: chain A residue 1138 LEU
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1239 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 98 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0070
   chunk 52 optimal weight:    0.8980
   chunk 109 optimal weight:    0.1980
   chunk 26 optimal weight:    0.4980
   chunk 110 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
A 217 ASN
A 407 ASN
A 711 ASN
A 715 ASN
** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.107664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.085023 restraints weight = 36087.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.087669 restraints weight = 20351.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.089455 restraints weight = 13987.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.090606 restraints weight = 10840.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.091407 restraints weight = 9135.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  10194  Z= 0.111
  Angle     :  0.619  14.566  13812  Z= 0.317
  Chirality :  0.045   0.164   1536
  Planarity :  0.004   0.054   1793
  Dihedral  :  5.862  81.604   1340
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 10.25 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 21.85 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.97 (0.23), residues: 1229
  helix:  0.09 (0.29), residues: 332
  sheet: -1.94 (0.48), residues: 100
  loop : -3.12 (0.19), residues: 797

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 863 
 TYR   0.022   0.001   TYR A1063 
 PHE   0.019   0.001   PHE A1067 
 TRP   0.027   0.001   TRP A1241 
 HIS   0.001   0.000   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (10193)
  covalent geometry    : angle       0.61852 (13810)
  SS BOND              : bond        0.01268 (    1)
  SS BOND              : angle       2.77281 (    2)
  hydrogen bonds       : bond        0.03371 (  248)
  hydrogen bonds       : angle       4.59972 (  678)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 126
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ASN cc_start: 0.8786 (t0) cc_final: 0.8149 (t0)
REVERT: A  123 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8460 (tm-30)
REVERT: A  578 ASN cc_start: 0.9041 (m110) cc_final: 0.8388 (p0)
REVERT: A  600 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8599 (m-80)
REVERT: A  637 ASN cc_start: 0.7666 (p0) cc_final: 0.7414 (p0)
REVERT: A  645 LEU cc_start: 0.7778 (mt) cc_final: 0.7467 (mt)
REVERT: A  657 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8021 (mm)
REVERT: A  758 LYS cc_start: 0.4646 (OUTLIER) cc_final: 0.4420 (pttm)
REVERT: A  870 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8004 (tt)
REVERT: A  930 LYS cc_start: 0.7508 (tppt) cc_final: 0.7273 (tppt)
REVERT: A 1022 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8484 (tt)
REVERT: A 1044 ASP cc_start: 0.9204 (p0) cc_final: 0.8973 (p0)
REVERT: A 1063 TYR cc_start: 0.7317 (m-80) cc_final: 0.6997 (m-80)
REVERT: A 1070 GLU cc_start: 0.4269 (tp30) cc_final: 0.3612 (tp30)
REVERT: A 1163 ASP cc_start: 0.7339 (t0) cc_final: 0.6974 (t0)
REVERT: A 1166 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.6360 (m-80)
REVERT: A 1201 PHE cc_start: 0.8848 (m-80) cc_final: 0.8640 (m-80)
  outliers start: 42
  outliers final: 24
  residues processed: 155
  average time/residue: 0.0916
  time to fit residues: 21.0476
Evaluate side-chains
  145 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 115
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  514 TYR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  727 ASN
Chi-restraints excluded: chain A residue  758 LYS
Chi-restraints excluded: chain A residue  870 LEU
Chi-restraints excluded: chain A residue  889 ILE
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  932 PHE
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1040 ILE
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1138 LEU
Chi-restraints excluded: chain A residue 1166 TYR
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1239 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 82 optimal weight:    0.0170
   chunk 73 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 104 optimal weight:    0.0170
   chunk 78 optimal weight:   10.0000
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.4258

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

Flipped N/Q/H residues before XYZ refinement:
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1107 ASN ** 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 = 0.4185 r_free = 0.4185 target = 0.108942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.086312 restraints weight = 35926.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.088986 restraints weight = 20062.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.090793 restraints weight = 13723.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.091945 restraints weight = 10628.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.092873 restraints weight = 8934.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
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   0.048  10194  Z= 0.105
  Angle     :  0.601  13.212  13812  Z= 0.308
  Chirality :  0.045   0.164   1536
  Planarity :  0.004   0.049   1793
  Dihedral  :  5.743  84.704   1340
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.50 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 22.56 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.76 (0.23), residues: 1229
  helix:  0.29 (0.30), residues: 329
  sheet: -1.85 (0.49), residues: 98
  loop : -2.98 (0.20), residues: 802

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 717 
 TYR   0.015   0.001   TYR A1023 
 PHE   0.021   0.001   PHE A 571 
 TRP   0.031   0.001   TRP A1241 
 HIS   0.001   0.000   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (10193)
  covalent geometry    : angle       0.60053 (13810)
  SS BOND              : bond        0.01053 (    1)
  SS BOND              : angle       2.30591 (    2)
  hydrogen bonds       : bond        0.03367 (  248)
  hydrogen bonds       : angle       4.43388 (  678)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 121
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6299 (mmm) cc_final: 0.5906 (mmm)
REVERT: A   55 ASN cc_start: 0.8762 (t0) cc_final: 0.7930 (t0)
REVERT: A  123 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8193 (tm-30)
REVERT: A  268 GLU cc_start: 0.8939 (tp30) cc_final: 0.8564 (mm-30)
REVERT: A  460 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.6403 (m-80)
REVERT: A  578 ASN cc_start: 0.9012 (m110) cc_final: 0.8368 (p0)
REVERT: A  600 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8577 (m-80)
REVERT: A  637 ASN cc_start: 0.7619 (p0) cc_final: 0.7367 (p0)
REVERT: A  645 LEU cc_start: 0.7828 (mt) cc_final: 0.7518 (mt)
REVERT: A  657 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8088 (mm)
REVERT: A  788 MET cc_start: 0.8485 (mmm) cc_final: 0.8133 (mmm)
REVERT: A  793 GLU cc_start: 0.9055 (tp30) cc_final: 0.8778 (tp30)
REVERT: A  870 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7904 (tt)
REVERT: A 1022 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8547 (tt)
REVERT: A 1044 ASP cc_start: 0.9201 (p0) cc_final: 0.8971 (p0)
REVERT: A 1063 TYR cc_start: 0.7215 (m-80) cc_final: 0.6996 (m-80)
REVERT: A 1070 GLU cc_start: 0.4460 (tp30) cc_final: 0.4142 (tp30)
REVERT: A 1163 ASP cc_start: 0.7401 (t0) cc_final: 0.7000 (t0)
REVERT: A 1166 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.6250 (m-80)
REVERT: A 1180 TYR cc_start: 0.8352 (t80) cc_final: 0.7644 (t80)
REVERT: A 1201 PHE cc_start: 0.8975 (m-80) cc_final: 0.8716 (m-80)
  outliers start: 42
  outliers final: 22
  residues processed: 153
  average time/residue: 0.0833
  time to fit residues: 19.3693
Evaluate side-chains
  137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  514 TYR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  727 ASN
Chi-restraints excluded: chain A residue  870 LEU
Chi-restraints excluded: chain A residue  889 ILE
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1040 ILE
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1125 ILE
Chi-restraints excluded: chain A residue 1166 TYR
Chi-restraints excluded: chain A residue 1237 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   chunk 117 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 45 optimal weight:    8.9990
   chunk 69 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN
A 903 ASN
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.107875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.085261 restraints weight = 36269.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.087875 restraints weight = 20541.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.089585 restraints weight = 14186.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.090830 restraints weight = 11058.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.091614 restraints weight = 9265.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.4396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10194  Z= 0.119
  Angle     :  0.619  12.381  13812  Z= 0.317
  Chirality :  0.045   0.155   1536
  Planarity :  0.003   0.049   1793
  Dihedral  :  5.497  94.127   1336
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.41 %
    Favored  : 89.59 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 23.88 %
    Favored  : 72.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.72 (0.23), residues: 1229
  helix:  0.36 (0.30), residues: 330
  sheet: -2.03 (0.48), residues: 100
  loop : -2.95 (0.20), residues: 799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 185 
 TYR   0.028   0.001   TYR A 743 
 PHE   0.017   0.001   PHE A 341 
 TRP   0.024   0.001   TRP A1241 
 HIS   0.002   0.000   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10193)
  covalent geometry    : angle       0.61853 (13810)
  SS BOND              : bond        0.00758 (    1)
  SS BOND              : angle       2.39637 (    2)
  hydrogen bonds       : bond        0.03361 (  248)
  hydrogen bonds       : angle       4.47671 (  678)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 114
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6327 (mmm) cc_final: 0.5850 (mmm)
REVERT: A   55 ASN cc_start: 0.8695 (t0) cc_final: 0.7796 (t0)
REVERT: A  123 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8450 (tm-30)
REVERT: A  130 TYR cc_start: 0.5766 (m-10) cc_final: 0.5233 (m-10)
REVERT: A  268 GLU cc_start: 0.8895 (tp30) cc_final: 0.8539 (mm-30)
REVERT: A  299 ILE cc_start: 0.9440 (tp) cc_final: 0.9233 (tt)
REVERT: A  460 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.6408 (m-80)
REVERT: A  578 ASN cc_start: 0.8994 (m110) cc_final: 0.8341 (p0)
REVERT: A  600 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8477 (m-80)
REVERT: A  637 ASN cc_start: 0.7593 (p0) cc_final: 0.7377 (p0)
REVERT: A  645 LEU cc_start: 0.7831 (mt) cc_final: 0.7495 (mt)
REVERT: A  657 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8086 (mm)
REVERT: A  788 MET cc_start: 0.8604 (mmm) cc_final: 0.8215 (mmm)
REVERT: A  793 GLU cc_start: 0.9031 (tp30) cc_final: 0.8760 (tp30)
REVERT: A  870 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8006 (tt)
REVERT: A  938 VAL cc_start: 0.9205 (t) cc_final: 0.8995 (m)
REVERT: A 1022 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8659 (tt)
REVERT: A 1044 ASP cc_start: 0.9185 (p0) cc_final: 0.8954 (p0)
REVERT: A 1063 TYR cc_start: 0.7334 (m-80) cc_final: 0.7128 (m-80)
REVERT: A 1070 GLU cc_start: 0.4279 (tp30) cc_final: 0.4001 (tp30)
REVERT: A 1163 ASP cc_start: 0.7435 (t0) cc_final: 0.7070 (t0)
REVERT: A 1166 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6232 (m-80)
  outliers start: 39
  outliers final: 25
  residues processed: 144
  average time/residue: 0.0803
  time to fit residues: 17.8749
Evaluate side-chains
  143 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 112
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  514 TYR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  727 ASN
Chi-restraints excluded: chain A residue  870 LEU
Chi-restraints excluded: chain A residue  889 ILE
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  932 PHE
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1040 ILE
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1125 ILE
Chi-restraints excluded: chain A residue 1138 LEU
Chi-restraints excluded: chain A residue 1166 TYR
Chi-restraints excluded: chain A residue 1237 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 111 optimal weight:   50.0000
   chunk 57 optimal weight:   10.0000
   chunk 97 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
A 829 ASN
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.105953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.082957 restraints weight = 36533.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.085545 restraints weight = 20806.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.087249 restraints weight = 14504.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.088442 restraints weight = 11399.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.089246 restraints weight = 9616.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.4785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10194  Z= 0.145
  Angle     :  0.638  11.840  13812  Z= 0.331
  Chirality :  0.046   0.155   1536
  Planarity :  0.004   0.047   1793
  Dihedral  :  5.652  98.023   1336
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.88 %
    Favored  : 88.04 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 24.58 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.78 (0.23), residues: 1229
  helix:  0.10 (0.29), residues: 332
  sheet: -1.84 (0.49), residues: 103
  loop : -2.92 (0.20), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 210 
 TYR   0.026   0.001   TYR A 743 
 PHE   0.023   0.002   PHE A 571 
 TRP   0.024   0.001   TRP A1241 
 HIS   0.002   0.001   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (10193)
  covalent geometry    : angle       0.63763 (13810)
  SS BOND              : bond        0.00510 (    1)
  SS BOND              : angle       2.60185 (    2)
  hydrogen bonds       : bond        0.03671 (  248)
  hydrogen bonds       : angle       4.60493 (  678)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 113
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6508 (mmm) cc_final: 0.5917 (mmm)
REVERT: A   55 ASN cc_start: 0.8733 (t0) cc_final: 0.8066 (t0)
REVERT: A  123 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8208 (tm-30)
REVERT: A  268 GLU cc_start: 0.8831 (tp30) cc_final: 0.8425 (mm-30)
REVERT: A  346 LYS cc_start: 0.8881 (tttm) cc_final: 0.8671 (ttpp)
REVERT: A  460 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.6403 (m-80)
REVERT: A  637 ASN cc_start: 0.7680 (p0) cc_final: 0.7446 (p0)
REVERT: A  645 LEU cc_start: 0.7950 (mt) cc_final: 0.7584 (mt)
REVERT: A  657 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7995 (mm)
REVERT: A  741 ASN cc_start: 0.9272 (m-40) cc_final: 0.8563 (p0)
REVERT: A  938 VAL cc_start: 0.9271 (t) cc_final: 0.9042 (m)
REVERT: A 1022 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8697 (tt)
REVERT: A 1044 ASP cc_start: 0.9203 (p0) cc_final: 0.8989 (p0)
REVERT: A 1063 TYR cc_start: 0.7367 (m-80) cc_final: 0.7147 (m-80)
REVERT: A 1073 GLU cc_start: 0.8432 (tp30) cc_final: 0.8218 (tp30)
REVERT: A 1163 ASP cc_start: 0.7479 (t0) cc_final: 0.7111 (t0)
REVERT: A 1166 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6861 (m-10)
REVERT: A 1180 TYR cc_start: 0.8470 (t80) cc_final: 0.8084 (m-80)
  outliers start: 40
  outliers final: 29
  residues processed: 144
  average time/residue: 0.0849
  time to fit residues: 18.4628
Evaluate side-chains
  139 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 106
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  109 ASN
Chi-restraints excluded: chain A residue  126 LYS
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  514 TYR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  727 ASN
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  854 ILE
Chi-restraints excluded: chain A residue  889 ILE
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  932 PHE
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1040 ILE
Chi-restraints excluded: chain A residue 1125 ILE
Chi-restraints excluded: chain A residue 1138 LEU
Chi-restraints excluded: chain A residue 1166 TYR
Chi-restraints excluded: chain A residue 1237 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 95 optimal weight:    5.9990
   chunk 91 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0870
   chunk 96 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   chunk 52 optimal weight:    0.0050
   chunk 77 optimal weight:    0.8980
   overall best weight:    1.5976

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
A 792 ASN
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.106236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.083224 restraints weight = 36508.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.085817 restraints weight = 20711.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.087538 restraints weight = 14414.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.088731 restraints weight = 11317.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.089566 restraints weight = 9554.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.4956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10194  Z= 0.135
  Angle     :  0.645  11.914  13812  Z= 0.330
  Chirality :  0.046   0.155   1536
  Planarity :  0.004   0.045   1793
  Dihedral  :  5.627  97.378   1336
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.64 %
    Favored  : 88.28 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 25.11 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.77 (0.23), residues: 1229
  helix:  0.10 (0.29), residues: 332
  sheet: -2.13 (0.49), residues: 99
  loop : -2.87 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 210 
 TYR   0.026   0.001   TYR A 743 
 PHE   0.016   0.001   PHE A1048 
 TRP   0.021   0.001   TRP A1241 
 HIS   0.002   0.000   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10193)
  covalent geometry    : angle       0.64448 (13810)
  SS BOND              : bond        0.01093 (    1)
  SS BOND              : angle       1.27268 (    2)
  hydrogen bonds       : bond        0.03643 (  248)
  hydrogen bonds       : angle       4.56920 (  678)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6413 (mmm) cc_final: 0.5976 (mmm)
REVERT: A  123 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8225 (tm-30)
REVERT: A  268 GLU cc_start: 0.8859 (tp30) cc_final: 0.8434 (mm-30)
REVERT: A  346 LYS cc_start: 0.8879 (tttm) cc_final: 0.8632 (ttpp)
REVERT: A  460 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.6381 (m-80)
REVERT: A  637 ASN cc_start: 0.7592 (p0) cc_final: 0.7335 (p0)
REVERT: A  645 LEU cc_start: 0.7973 (mt) cc_final: 0.7611 (mt)
REVERT: A  657 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7954 (mm)
REVERT: A  741 ASN cc_start: 0.9306 (m-40) cc_final: 0.8630 (p0)
REVERT: A  938 VAL cc_start: 0.9236 (t) cc_final: 0.8996 (m)
REVERT: A 1022 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8677 (tt)
REVERT: A 1044 ASP cc_start: 0.9202 (p0) cc_final: 0.8993 (p0)
REVERT: A 1163 ASP cc_start: 0.7498 (t0) cc_final: 0.7131 (t0)
REVERT: A 1166 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.6917 (m-10)
  outliers start: 31
  outliers final: 25
  residues processed: 137
  average time/residue: 0.0835
  time to fit residues: 17.2515
Evaluate side-chains
  133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  109 ASN
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue  514 TYR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  727 ASN
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  889 ILE
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1040 ILE
Chi-restraints excluded: chain A residue 1138 LEU
Chi-restraints excluded: chain A residue 1166 TYR
Chi-restraints excluded: chain A residue 1237 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 114 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0970
   chunk 22 optimal weight:    0.8980
   chunk 79 optimal weight:    0.0050
   chunk 20 optimal weight:    0.5980
   chunk 111 optimal weight:    9.9990
   chunk 25 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   overall best weight:    0.4592

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

Flipped N/Q/H residues before XYZ refinement:
A 792 ASN
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 973 HIS ** 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 = 0.4180 r_free = 0.4180 target = 0.108723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.087298 restraints weight = 35704.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.090214 restraints weight = 18812.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.091586 restraints weight = 12131.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.092037 restraints weight = 10195.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.092324 restraints weight = 8840.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.5075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  10194  Z= 0.118
  Angle     :  0.674  12.032  13812  Z= 0.342
  Chirality :  0.046   0.176   1536
  Planarity :  0.004   0.049   1793
  Dihedral  :  5.657 102.021   1336
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 10.09 %
    Favored  : 89.83 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 25.55 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.68 (0.23), residues: 1229
  helix:  0.20 (0.29), residues: 335
  sheet: -2.35 (0.52), residues: 89
  loop : -2.79 (0.20), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 863 
 TYR   0.026   0.001   TYR A 743 
 PHE   0.016   0.001   PHE A 211 
 TRP   0.027   0.001   TRP A1241 
 HIS   0.002   0.000   HIS A1175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (10193)
  covalent geometry    : angle       0.67371 (13810)
  SS BOND              : bond        0.02638 (    1)
  SS BOND              : angle       1.79622 (    2)
  hydrogen bonds       : bond        0.03344 (  248)
  hydrogen bonds       : angle       4.38331 (  678)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6315 (mmm) cc_final: 0.5958 (mmm)
REVERT: A   55 ASN cc_start: 0.8678 (t0) cc_final: 0.7821 (t0)
REVERT: A  123 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8478 (tm-30)
REVERT: A  268 GLU cc_start: 0.8875 (tp30) cc_final: 0.8511 (mm-30)
REVERT: A  346 LYS cc_start: 0.8861 (tttm) cc_final: 0.8609 (ttpp)
REVERT: A  460 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.6377 (m-80)
REVERT: A  637 ASN cc_start: 0.7646 (p0) cc_final: 0.7360 (p0)
REVERT: A  645 LEU cc_start: 0.7896 (mt) cc_final: 0.7556 (mt)
REVERT: A  657 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8045 (mm)
REVERT: A  741 ASN cc_start: 0.9321 (m-40) cc_final: 0.8658 (p0)
REVERT: A  788 MET cc_start: 0.8478 (mmm) cc_final: 0.8084 (mmm)
REVERT: A  856 TYR cc_start: 0.8535 (m-80) cc_final: 0.8236 (m-80)
REVERT: A  938 VAL cc_start: 0.9177 (t) cc_final: 0.8943 (m)
REVERT: A 1044 ASP cc_start: 0.9209 (p0) cc_final: 0.8988 (p0)
REVERT: A 1163 ASP cc_start: 0.7485 (t0) cc_final: 0.7027 (t0)
REVERT: A 1166 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.7029 (m-10)
  outliers start: 26
  outliers final: 18
  residues processed: 139
  average time/residue: 0.0800
  time to fit residues: 17.1057
Evaluate side-chains
  129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  514 TYR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  727 ASN
Chi-restraints excluded: chain A residue  889 ILE
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue 1040 ILE
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1166 TYR
Chi-restraints excluded: chain A residue 1237 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 6 optimal weight:    0.0570
   chunk 33 optimal weight:    0.6980
   chunk 103 optimal weight:    0.6980
   chunk 62 optimal weight:    9.9990
   chunk 114 optimal weight:    7.9990
   chunk 110 optimal weight:   20.0000
   chunk 1 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 118 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.8902

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

Flipped N/Q/H residues before XYZ refinement:
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 973 HIS ** 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 = 0.4169 r_free = 0.4169 target = 0.107931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.085511 restraints weight = 35887.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.088117 restraints weight = 20163.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.089888 restraints weight = 13852.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.091026 restraints weight = 10739.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.091892 restraints weight = 9055.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.5186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10194  Z= 0.120
  Angle     :  0.675  11.933  13812  Z= 0.340
  Chirality :  0.046   0.202   1536
  Planarity :  0.003   0.051   1793
  Dihedral  :  4.779  29.067   1333
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 10.82 %
    Favored  : 89.10 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 26.26 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.59 (0.23), residues: 1229
  helix:  0.35 (0.30), residues: 330
  sheet: -2.35 (0.58), residues: 70
  loop : -2.75 (0.20), residues: 829

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 863 
 TYR   0.027   0.001   TYR A 743 
 PHE   0.016   0.001   PHE A1067 
 TRP   0.021   0.001   TRP A1241 
 HIS   0.001   0.000   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (10193)
  covalent geometry    : angle       0.67449 (13810)
  SS BOND              : bond        0.00480 (    1)
  SS BOND              : angle       2.24862 (    2)
  hydrogen bonds       : bond        0.03344 (  248)
  hydrogen bonds       : angle       4.41054 (  678)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2037.29 seconds
wall clock time: 36 minutes 2.58 seconds (2162.58 seconds total)