Starting phenix.real_space_refine
on Mon Jul 28 06:32:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qfp_13946/07_2025/7qfp_13946.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qfp_13946/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qfp_13946/07_2025/7qfp_13946.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qfp_13946/07_2025/7qfp_13946.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qfp_13946/07_2025/7qfp_13946.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qfp_13946/07_2025/7qfp_13946.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.15, per 1000 atoms: 0.62
  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: 2.70
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 1.14
  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: 3.83

  Time building geometry restraints manager: 3.19 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:             1.660
  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:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     27.050
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.480
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.009   0.001   TRP A 937 
 HIS   0.004   0.001   HIS A 229 
 PHE   0.012   0.001   PHE A 905 
 TYR   0.021   0.002   TYR A 233 
 ARG   0.004   0.000   ARG A 863 

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

*********************** 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  : 1.193 
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: 0.7720 (mm-30)
REVERT: A  442 ILE cc_start: 0.8815 (tt) cc_final: 0.8204 (tt)
REVERT: A  503 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7836 (pm20)
REVERT: A  578 ASN cc_start: 0.9012 (m110) cc_final: 0.8456 (p0)
REVERT: A  637 ASN cc_start: 0.7768 (p0) cc_final: 0.7498 (p0)
REVERT: A  645 LEU cc_start: 0.7880 (mt) cc_final: 0.7608 (mt)
REVERT: A  689 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8567 (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: 0.4486 (pttm)
REVERT: A  870 LEU cc_start: 0.8615 (tp) cc_final: 0.8403 (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: 0.7918 (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: 0.7429 (t80)
REVERT: A 1163 ASP cc_start: 0.7158 (t0) cc_final: 0.6800 (t0)
REVERT: A 1201 PHE cc_start: 0.8283 (m-80) cc_final: 0.7550 (m-80)
  outliers start: 47
  outliers final: 15
  residues processed: 252
  average time/residue: 0.2322
  time to fit residues: 81.3683
Evaluate side-chains
  146 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
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 103 optimal weight:    0.6980
   chunk 93 optimal weight:    7.9990
   chunk 51 optimal weight:    0.0970
   chunk 31 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 96 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 71 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 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 685 ASN
A 711 ASN
A 715 ASN
A 727 ASN
A 765 ASN
A 805 ASN
A 837 ASN
A 871 ASN
A 952 ASN
A1025 ASN
** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1203 GLN
A1251 ASN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.110381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.088156 restraints weight = 35321.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.090858 restraints weight = 19497.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.092711 restraints weight = 13204.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.2161

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= 0.133
  Angle     :  0.669   7.699  13812  Z= 0.357
  Chirality :  0.047   0.179   1536
  Planarity :  0.004   0.065   1793
  Dihedral  :  7.352  74.654   1377
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 10.33 %
    Favored  : 89.59 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 17.89 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.78 (0.20), residues: 1229
  helix: -1.20 (0.26), residues: 327
  sheet: -2.29 (0.45), residues: 108
  loop : -3.34 (0.18), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1241 
 HIS   0.002   0.001   HIS A 229 
 PHE   0.030   0.002   PHE A 670 
 TYR   0.020   0.001   TYR A1023 
 ARG   0.005   0.001   ARG A 873 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04323 (  248)
  hydrogen bonds       : angle       5.38258 (  678)
  SS BOND              : bond        0.00516 (    1)
  SS BOND              : angle       1.80629 (    2)
  covalent geometry    : bond        0.00283 (10193)
  covalent geometry    : angle       0.66852 (13810)

*********************** 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
  184 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 144
  time to evaluate  : 1.099 
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: A   53 MET cc_start: 0.5730 (mmm) cc_final: 0.5380 (mmm)
REVERT: A  158 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8162 (mm110)
REVERT: A  266 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8649 (mt)
REVERT: A  555 THR cc_start: 0.6948 (OUTLIER) cc_final: 0.6666 (t)
REVERT: A  578 ASN cc_start: 0.8976 (m110) cc_final: 0.8379 (p0)
REVERT: A  600 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8684 (m-80)
REVERT: A  637 ASN cc_start: 0.7784 (p0) cc_final: 0.7534 (p0)
REVERT: A  645 LEU cc_start: 0.7925 (mt) cc_final: 0.7648 (mt)
REVERT: A  689 LYS cc_start: 0.9171 (mmmm) cc_final: 0.8587 (pttt)
REVERT: A  758 LYS cc_start: 0.4571 (OUTLIER) cc_final: 0.4135 (pttm)
REVERT: A  870 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8160 (tt)
REVERT: A 1022 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7647 (tt)
REVERT: A 1044 ASP cc_start: 0.9176 (p0) cc_final: 0.8860 (p0)
REVERT: A 1076 ILE cc_start: 0.8231 (mm) cc_final: 0.8011 (mm)
REVERT: A 1163 ASP cc_start: 0.7080 (t0) cc_final: 0.6714 (t0)
  outliers start: 40
  outliers final: 17
  residues processed: 169
  average time/residue: 0.2187
  time to fit residues: 53.1854
Evaluate side-chains
  132 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
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  266 ILE
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  443 CYS
Chi-restraints excluded: chain A residue  447 ASN
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  514 TYR
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  600 PHE
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  870 LEU
Chi-restraints excluded: chain A residue  938 VAL
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 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 18 optimal weight:    8.9990
   chunk 24 optimal weight:    8.9990
   chunk 30 optimal weight:    8.9990
   chunk 94 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 79 optimal weight:    8.9990
   chunk 122 optimal weight:    6.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 510 GLN
A 634 GLN
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 945 ASN
A 952 ASN
A 981 GLN
A1041 HIS
** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1224 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.100681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.078459 restraints weight = 37439.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.080814 restraints weight = 21721.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.082314 restraints weight = 15321.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.3920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.087  10194  Z= 0.313
  Angle     :  0.832  15.150  13812  Z= 0.440
  Chirality :  0.050   0.186   1536
  Planarity :  0.005   0.074   1793
  Dihedral  :  7.023  74.502   1350
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 18.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 14.89 %
    Favored  : 85.03 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 20.53 %
    Favored  : 74.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.77 (0.21), residues: 1229
  helix: -1.10 (0.26), residues: 337
  sheet: -2.36 (0.47), residues: 98
  loop : -3.40 (0.19), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A1241 
 HIS   0.004   0.001   HIS A  73 
 PHE   0.025   0.003   PHE A1114 
 TYR   0.024   0.002   TYR A 324 
 ARG   0.010   0.001   ARG A 863 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05032 (  248)
  hydrogen bonds       : angle       5.68982 (  678)
  SS BOND              : bond        0.05806 (    1)
  SS BOND              : angle       8.02437 (    2)
  covalent geometry    : bond        0.00691 (10193)
  covalent geometry    : angle       0.82599 (13810)

*********************** 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
  158 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 100
  time to evaluate  : 1.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6665 (mmm) cc_final: 0.6200 (mmm)
REVERT: A  123 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8371 (tm-30)
REVERT: A  324 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7339 (p90)
REVERT: A  460 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.6699 (m-80)
REVERT: A  645 LEU cc_start: 0.8108 (mt) cc_final: 0.7761 (mt)
REVERT: A  758 LYS cc_start: 0.4564 (OUTLIER) cc_final: 0.4342 (pttm)
REVERT: A  930 LYS cc_start: 0.8267 (tppt) cc_final: 0.8060 (tppt)
REVERT: A 1022 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8701 (tt)
REVERT: A 1044 ASP cc_start: 0.9168 (p0) cc_final: 0.8870 (p0)
REVERT: A 1070 GLU cc_start: 0.4644 (tp30) cc_final: 0.4251 (tp30)
REVERT: A 1077 GLN cc_start: 0.8567 (mp10) cc_final: 0.8332 (pm20)
REVERT: A 1163 ASP cc_start: 0.7430 (t0) cc_final: 0.6981 (t0)
REVERT: A 1207 MET cc_start: 0.5467 (OUTLIER) cc_final: 0.5059 (mtt)
REVERT: A 1241 TRP cc_start: 0.8257 (p-90) cc_final: 0.7995 (p-90)
  outliers start: 58
  outliers final: 30
  residues processed: 147
  average time/residue: 0.2785
  time to fit residues: 61.1285
Evaluate side-chains
  125 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 90
  time to evaluate  : 1.947 
-------------------------------------------------------------------------------
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  211 PHE
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  324 TYR
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  446 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  500 LEU
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  555 THR
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  690 GLU
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  834 ASP
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  940 ILE
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 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 1207 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 51 optimal weight:    0.3980
   chunk 64 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 108 optimal weight:   20.0000
   chunk 50 optimal weight:    1.9990
   chunk 110 optimal weight:   20.0000
   overall best weight:    2.6788

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

Flipped N/Q/H residues before XYZ refinement:
A 382 ASN
A 903 ASN
** 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 = 0.4070 r_free = 0.4070 target = 0.102309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.079696 restraints weight = 36887.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.082063 restraints weight = 21148.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.083729 restraints weight = 14860.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.4316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10194  Z= 0.182
  Angle     :  0.681  13.343  13812  Z= 0.357
  Chirality :  0.046   0.155   1536
  Planarity :  0.004   0.060   1793
  Dihedral  :  6.542  75.915   1344
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 12.04 %
    Favored  : 87.88 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 22.20 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.54 (0.22), residues: 1229
  helix: -0.62 (0.28), residues: 331
  sheet: -2.30 (0.47), residues: 99
  loop : -3.37 (0.19), residues: 799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 937 
 HIS   0.002   0.001   HIS A  73 
 PHE   0.018   0.002   PHE A1114 
 TYR   0.018   0.002   TYR A1023 
 ARG   0.005   0.001   ARG A 863 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04323 (  248)
  hydrogen bonds       : angle       5.22618 (  678)
  SS BOND              : bond        0.01262 (    1)
  SS BOND              : angle       3.75125 (    2)
  covalent geometry    : bond        0.00410 (10193)
  covalent geometry    : angle       0.67945 (13810)

*********************** 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
  159 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 106
  time to evaluate  : 1.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6836 (mmm) cc_final: 0.6360 (mmm)
REVERT: A  123 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8207 (tm-30)
REVERT: A  228 MET cc_start: 0.9001 (mtt) cc_final: 0.8423 (mmt)
REVERT: A  460 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.6374 (m-80)
REVERT: A  645 LEU cc_start: 0.7913 (mt) cc_final: 0.7619 (mt)
REVERT: A  721 MET cc_start: 0.8639 (tpp) cc_final: 0.7989 (mmp)
REVERT: A  981 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6957 (tm-30)
REVERT: A 1022 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8798 (tt)
REVERT: A 1044 ASP cc_start: 0.9225 (p0) cc_final: 0.9018 (p0)
REVERT: A 1063 TYR cc_start: 0.7438 (m-80) cc_final: 0.7164 (m-80)
REVERT: A 1070 GLU cc_start: 0.4528 (tp30) cc_final: 0.4201 (tp30)
REVERT: A 1163 ASP cc_start: 0.7506 (t0) cc_final: 0.7194 (t0)
REVERT: A 1241 TRP cc_start: 0.8307 (p-90) cc_final: 0.8009 (p-90)
  outliers start: 53
  outliers final: 34
  residues processed: 148
  average time/residue: 0.2075
  time to fit residues: 44.8024
Evaluate side-chains
  129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 92
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
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  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  396 ASN
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  446 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  488 VAL
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  661 THR
Chi-restraints excluded: chain A residue  690 GLU
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  868 SER
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  932 PHE
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  938 VAL
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  981 GLN
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1040 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 62 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 78 optimal weight:   20.0000
   chunk 32 optimal weight:    4.9990
   chunk 106 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 59 optimal weight:    0.2980
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 407 ASN
A 829 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.103019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.080468 restraints weight = 36608.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.082928 restraints weight = 20889.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.084587 restraints weight = 14515.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.4606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10194  Z= 0.148
  Angle     :  0.653  12.824  13812  Z= 0.337
  Chirality :  0.046   0.158   1536
  Planarity :  0.004   0.048   1793
  Dihedral  :  5.916  75.922   1338
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 13.18 %
    Favored  : 86.74 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 22.47 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.30 (0.22), residues: 1229
  helix: -0.30 (0.29), residues: 329
  sheet: -2.27 (0.48), residues: 99
  loop : -3.25 (0.20), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1241 
 HIS   0.002   0.001   HIS A  73 
 PHE   0.017   0.002   PHE A1114 
 TYR   0.028   0.001   TYR A1180 
 ARG   0.004   0.001   ARG A 863 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03949 (  248)
  hydrogen bonds       : angle       4.95812 (  678)
  SS BOND              : bond        0.01407 (    1)
  SS BOND              : angle       2.52794 (    2)
  covalent geometry    : bond        0.00333 (10193)
  covalent geometry    : angle       0.65248 (13810)

*********************** 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
  163 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 106
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8235 (tm-30)
REVERT: A  228 MET cc_start: 0.8947 (mtt) cc_final: 0.8409 (mmt)
REVERT: A  460 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.6353 (m-80)
REVERT: A  600 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8535 (m-80)
REVERT: A  645 LEU cc_start: 0.7827 (mt) cc_final: 0.7523 (mt)
REVERT: A  721 MET cc_start: 0.8647 (tpp) cc_final: 0.8002 (mmp)
REVERT: A  870 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8410 (tt)
REVERT: A  898 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8349 (m-10)
REVERT: A  930 LYS cc_start: 0.7789 (tppt) cc_final: 0.7581 (tppt)
REVERT: A 1044 ASP cc_start: 0.9198 (p0) cc_final: 0.8985 (p0)
REVERT: A 1063 TYR cc_start: 0.7502 (m-80) cc_final: 0.7240 (m-80)
REVERT: A 1070 GLU cc_start: 0.4530 (tp30) cc_final: 0.4121 (tp30)
REVERT: A 1163 ASP cc_start: 0.7477 (t0) cc_final: 0.7157 (t0)
REVERT: A 1241 TRP cc_start: 0.8317 (p-90) cc_final: 0.7864 (p-90)
REVERT: A 1257 TRP cc_start: 0.5974 (m100) cc_final: 0.5669 (m100)
  outliers start: 57
  outliers final: 40
  residues processed: 152
  average time/residue: 0.2167
  time to fit residues: 48.3495
Evaluate side-chains
  142 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 98
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
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  162 LEU
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  281 THR
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  446 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  488 VAL
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  552 VAL
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  690 GLU
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  727 ASN
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  868 SER
Chi-restraints excluded: chain A residue  870 LEU
Chi-restraints excluded: chain A residue  898 TYR
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  932 PHE
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  938 VAL
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue 1040 ILE
Chi-restraints excluded: chain A residue 1106 LEU
Chi-restraints excluded: chain A residue 1125 ILE
Chi-restraints excluded: chain A residue 1138 LEU
Chi-restraints excluded: chain A residue 1231 PHE
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 37 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 69 optimal weight:    9.9990
   chunk 104 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0470
   chunk 111 optimal weight:    8.9990
   chunk 89 optimal weight:    6.9990
   chunk 76 optimal weight:    0.2980
   overall best weight:    1.0282

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

Flipped N/Q/H residues before XYZ refinement:
A 217 ASN
** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.105126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.082279 restraints weight = 36386.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.084862 restraints weight = 20506.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.086568 restraints weight = 14186.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.4732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10194  Z= 0.119
  Angle     :  0.645  12.068  13812  Z= 0.328
  Chirality :  0.045   0.158   1536
  Planarity :  0.003   0.049   1793
  Dihedral  :  5.809  82.455   1338
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.47 %
    Favored  : 88.45 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 24.32 %
    Favored  : 71.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.09 (0.23), residues: 1229
  helix: -0.06 (0.30), residues: 328
  sheet: -2.06 (0.48), residues: 97
  loop : -3.15 (0.20), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 978 
 HIS   0.001   0.000   HIS A 817 
 PHE   0.020   0.001   PHE A 571 
 TYR   0.015   0.001   TYR A1023 
 ARG   0.003   0.000   ARG A 863 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03681 (  248)
  hydrogen bonds       : angle       4.76590 (  678)
  SS BOND              : bond        0.01136 (    1)
  SS BOND              : angle       2.37498 (    2)
  covalent geometry    : bond        0.00268 (10193)
  covalent geometry    : angle       0.64476 (13810)

*********************** 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
  151 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 106
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8249 (tm-30)
REVERT: A  460 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.6335 (m-80)
REVERT: A  600 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8490 (m-80)
REVERT: A  645 LEU cc_start: 0.7828 (mt) cc_final: 0.7509 (mt)
REVERT: A  721 MET cc_start: 0.8620 (tpp) cc_final: 0.7936 (mmp)
REVERT: A  741 ASN cc_start: 0.9392 (m-40) cc_final: 0.8836 (p0)
REVERT: A  788 MET cc_start: 0.8594 (mmm) cc_final: 0.8326 (mmm)
REVERT: A  856 TYR cc_start: 0.8270 (m-80) cc_final: 0.7716 (m-80)
REVERT: A  870 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8096 (mm)
REVERT: A  898 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.8306 (m-10)
REVERT: A  903 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8073 (t0)
REVERT: A 1044 ASP cc_start: 0.9224 (p0) cc_final: 0.9009 (p0)
REVERT: A 1063 TYR cc_start: 0.7378 (m-80) cc_final: 0.7119 (m-80)
REVERT: A 1070 GLU cc_start: 0.4664 (tp30) cc_final: 0.4373 (tp30)
REVERT: A 1163 ASP cc_start: 0.7508 (t0) cc_final: 0.7138 (t0)
REVERT: A 1241 TRP cc_start: 0.8532 (p-90) cc_final: 0.8186 (p-90)
  outliers start: 45
  outliers final: 32
  residues processed: 144
  average time/residue: 0.2033
  time to fit residues: 43.0352
Evaluate side-chains
  134 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 97
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
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  446 ILE
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  488 VAL
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  552 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  690 GLU
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  868 SER
Chi-restraints excluded: chain A residue  870 LEU
Chi-restraints excluded: chain A residue  898 TYR
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  903 ASN
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  932 PHE
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  938 VAL
Chi-restraints excluded: chain A residue  976 ILE
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 1239 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 109 optimal weight:   20.0000
   chunk 21 optimal weight:    3.9990
   chunk 122 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0980
   chunk 56 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    2.4188

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

Flipped N/Q/H residues before XYZ refinement:
** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 892 ASN
A 904 GLN
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 983 ASN
** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.102552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.079829 restraints weight = 36819.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.082274 restraints weight = 21014.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.083967 restraints weight = 14608.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.5049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10194  Z= 0.172
  Angle     :  0.691  11.696  13812  Z= 0.354
  Chirality :  0.046   0.158   1536
  Planarity :  0.004   0.045   1793
  Dihedral  :  5.987  88.944   1338
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.59 %
    Favored  : 86.41 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 24.14 %
    Favored  : 70.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.23), residues: 1229
  helix: -0.10 (0.30), residues: 328
  sheet: -2.27 (0.46), residues: 107
  loop : -3.17 (0.20), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  57 
 HIS   0.002   0.001   HIS A1041 
 PHE   0.013   0.002   PHE A1048 
 TYR   0.028   0.002   TYR A1180 
 ARG   0.005   0.000   ARG A 863 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  248)
  hydrogen bonds       : angle       4.89176 (  678)
  SS BOND              : bond        0.00998 (    1)
  SS BOND              : angle       2.77946 (    2)
  covalent geometry    : bond        0.00386 (10193)
  covalent geometry    : angle       0.69006 (13810)

*********************** 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: 57
    poor density    : 96
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8252 (tm-30)
REVERT: A  460 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.6381 (m-80)
REVERT: A  600 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8419 (m-80)
REVERT: A  645 LEU cc_start: 0.7889 (mt) cc_final: 0.7549 (mt)
REVERT: A  721 MET cc_start: 0.8643 (tpp) cc_final: 0.8004 (mmp)
REVERT: A  741 ASN cc_start: 0.9392 (m-40) cc_final: 0.8873 (p0)
REVERT: A  898 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8452 (m-10)
REVERT: A  903 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8145 (t0)
REVERT: A  930 LYS cc_start: 0.7937 (tppt) cc_final: 0.7715 (tppt)
REVERT: A  946 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8897 (tptp)
REVERT: A 1044 ASP cc_start: 0.9214 (p0) cc_final: 0.9012 (p0)
REVERT: A 1063 TYR cc_start: 0.7309 (m-80) cc_final: 0.7044 (m-80)
REVERT: A 1070 GLU cc_start: 0.4416 (tp30) cc_final: 0.3982 (tp30)
REVERT: A 1163 ASP cc_start: 0.7576 (t0) cc_final: 0.7205 (t0)
REVERT: A 1241 TRP cc_start: 0.8445 (p-90) cc_final: 0.8087 (p-90)
  outliers start: 57
  outliers final: 42
  residues processed: 144
  average time/residue: 0.2096
  time to fit residues: 44.2257
Evaluate side-chains
  138 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 91
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
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  278 ASN
Chi-restraints excluded: chain A residue  281 THR
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  446 ILE
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  488 VAL
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  552 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  600 PHE
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  640 ASP
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  690 GLU
Chi-restraints excluded: chain A residue  698 VAL
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  868 SER
Chi-restraints excluded: chain A residue  892 ASN
Chi-restraints excluded: chain A residue  898 TYR
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  903 ASN
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  932 PHE
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  938 VAL
Chi-restraints excluded: chain A residue  946 LYS
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue 1040 ILE
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1125 ILE
Chi-restraints excluded: chain A residue 1138 LEU
Chi-restraints excluded: chain A residue 1231 PHE
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1239 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0370
   chunk 38 optimal weight:    0.0030
   chunk 7 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 114 optimal weight:    0.0670
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.3806

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 892 ASN
A 958 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.107207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.084226 restraints weight = 35356.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.086846 restraints weight = 19988.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.088639 restraints weight = 13812.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.5117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052  10194  Z= 0.115
  Angle     :  0.671  11.726  13812  Z= 0.337
  Chirality :  0.046   0.168   1536
  Planarity :  0.004   0.052   1793
  Dihedral  :  5.789  92.493   1338
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.50 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 25.99 %
    Favored  : 70.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.23), residues: 1229
  helix: -0.06 (0.29), residues: 334
  sheet: -2.07 (0.48), residues: 95
  loop : -3.09 (0.20), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1241 
 HIS   0.001   0.000   HIS A 817 
 PHE   0.018   0.002   PHE A 571 
 TYR   0.021   0.001   TYR A 743 
 ARG   0.002   0.000   ARG A 411 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03483 (  248)
  hydrogen bonds       : angle       4.54840 (  678)
  SS BOND              : bond        0.00902 (    1)
  SS BOND              : angle       2.15728 (    2)
  covalent geometry    : bond        0.00247 (10193)
  covalent geometry    : angle       0.67026 (13810)

*********************** 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
  140 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 1.180 
Fit side-chains
REVERT: A  123 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8545 (tm-30)
REVERT: A  460 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.6299 (m-80)
REVERT: A  503 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6904 (pm20)
REVERT: A  645 LEU cc_start: 0.7916 (mt) cc_final: 0.7590 (mt)
REVERT: A  741 ASN cc_start: 0.9332 (m-40) cc_final: 0.8776 (p0)
REVERT: A  903 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8074 (t0)
REVERT: A  946 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8945 (tptp)
REVERT: A 1044 ASP cc_start: 0.9236 (p0) cc_final: 0.9026 (p0)
REVERT: A 1063 TYR cc_start: 0.7291 (m-80) cc_final: 0.7042 (m-80)
REVERT: A 1070 GLU cc_start: 0.4529 (tp30) cc_final: 0.4004 (tp30)
REVERT: A 1163 ASP cc_start: 0.7521 (t0) cc_final: 0.7065 (t0)
REVERT: A 1241 TRP cc_start: 0.8187 (p-90) cc_final: 0.7743 (p-90)
  outliers start: 36
  outliers final: 23
  residues processed: 136
  average time/residue: 0.1980
  time to fit residues: 40.0096
Evaluate side-chains
  119 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
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  298 LYS
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  351 PHE
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  446 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  690 GLU
Chi-restraints excluded: chain A residue  758 LYS
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  903 ASN
Chi-restraints excluded: chain A residue  917 ILE
Chi-restraints excluded: chain A residue  946 LYS
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 1237 VAL
Chi-restraints excluded: chain A residue 1239 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 71 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 89 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 84 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 958 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.104417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.081504 restraints weight = 37472.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.084008 restraints weight = 21499.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.085680 restraints weight = 15067.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.5295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10194  Z= 0.150
  Angle     :  0.675  11.516  13812  Z= 0.343
  Chirality :  0.046   0.161   1536
  Planarity :  0.004   0.045   1793
  Dihedral  :  5.869  97.308   1338
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.86 %
    Favored  : 87.14 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 26.61 %
    Favored  : 70.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.23), residues: 1229
  helix: -0.09 (0.30), residues: 336
  sheet: -2.10 (0.47), residues: 105
  loop : -3.12 (0.20), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  57 
 HIS   0.002   0.001   HIS A1264 
 PHE   0.019   0.002   PHE A 571 
 TYR   0.027   0.001   TYR A1180 
 ARG   0.003   0.000   ARG A 863 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03650 (  248)
  hydrogen bonds       : angle       4.64658 (  678)
  SS BOND              : bond        0.00903 (    1)
  SS BOND              : angle       2.46200 (    2)
  covalent geometry    : bond        0.00338 (10193)
  covalent geometry    : angle       0.67454 (13810)

*********************** 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
  134 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 99
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8233 (tm-30)
REVERT: A  228 MET cc_start: 0.8965 (mtt) cc_final: 0.8560 (mmt)
REVERT: A  460 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.6372 (m-80)
REVERT: A  645 LEU cc_start: 0.7975 (mt) cc_final: 0.7623 (mt)
REVERT: A  741 ASN cc_start: 0.9350 (m-40) cc_final: 0.8763 (p0)
REVERT: A  903 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8097 (t0)
REVERT: A  960 MET cc_start: 0.6051 (mmp) cc_final: 0.5591 (ppp)
REVERT: A 1063 TYR cc_start: 0.7288 (m-80) cc_final: 0.7072 (m-80)
REVERT: A 1163 ASP cc_start: 0.7603 (t0) cc_final: 0.7204 (t0)
REVERT: A 1241 TRP cc_start: 0.8248 (p-90) cc_final: 0.7804 (p-90)
  outliers start: 35
  outliers final: 28
  residues processed: 131
  average time/residue: 0.2099
  time to fit residues: 39.9540
Evaluate side-chains
  124 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
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  162 LEU
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  348 LEU
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  446 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  609 THR
Chi-restraints excluded: chain A residue  640 ASP
Chi-restraints excluded: chain A residue  690 GLU
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  889 ILE
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  903 ASN
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 1237 VAL
Chi-restraints excluded: chain A residue 1239 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 55 optimal weight:    8.9990
   chunk 81 optimal weight:   20.0000
   chunk 109 optimal weight:    0.9980
   chunk 87 optimal weight:    0.0980
   chunk 90 optimal weight:    0.0770
   chunk 106 optimal weight:    5.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 140 GLN
** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1041 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.107478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.084493 restraints weight = 35977.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.087121 restraints weight = 20356.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.088883 restraints weight = 14146.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.5364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10194  Z= 0.115
  Angle     :  0.668  11.555  13812  Z= 0.335
  Chirality :  0.046   0.158   1536
  Planarity :  0.004   0.072   1793
  Dihedral  :  5.784 101.308   1338
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.47 %
    Favored  : 88.53 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 26.43 %
    Favored  : 70.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.23), residues: 1229
  helix:  0.10 (0.30), residues: 329
  sheet: -2.17 (0.46), residues: 110
  loop : -2.98 (0.20), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1241 
 HIS   0.008   0.001   HIS A1041 
 PHE   0.016   0.001   PHE A 571 
 TYR   0.016   0.001   TYR A1023 
 ARG   0.003   0.000   ARG A 863 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03341 (  248)
  hydrogen bonds       : angle       4.46317 (  678)
  SS BOND              : bond        0.00826 (    1)
  SS BOND              : angle       2.09009 (    2)
  covalent geometry    : bond        0.00254 (10193)
  covalent geometry    : angle       0.66739 (13810)

********************** 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
  134 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8556 (tm-30)
REVERT: A  268 GLU cc_start: 0.8854 (tp30) cc_final: 0.8330 (mm-30)
REVERT: A  460 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.6303 (m-80)
REVERT: A  600 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8457 (m-80)
REVERT: A  645 LEU cc_start: 0.7926 (mt) cc_final: 0.7571 (mt)
REVERT: A  741 ASN cc_start: 0.9347 (m-40) cc_final: 0.8730 (p0)
REVERT: A  903 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8125 (t0)
REVERT: A 1063 TYR cc_start: 0.7264 (m-80) cc_final: 0.6999 (m-80)
REVERT: A 1163 ASP cc_start: 0.7472 (t0) cc_final: 0.6847 (t0)
REVERT: A 1207 MET cc_start: 0.5721 (mtt) cc_final: 0.5333 (mtt)
REVERT: A 1216 MET cc_start: 0.2899 (mmm) cc_final: 0.2619 (mmt)
REVERT: A 1241 TRP cc_start: 0.8198 (p-90) cc_final: 0.7754 (p-90)
  outliers start: 32
  outliers final: 23
  residues processed: 129
  average time/residue: 0.1909
  time to fit residues: 37.4076
Evaluate side-chains
  124 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
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  298 LYS
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  351 PHE
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  446 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  600 PHE
Chi-restraints excluded: chain A residue  609 THR
Chi-restraints excluded: chain A residue  640 ASP
Chi-restraints excluded: chain A residue  690 GLU
Chi-restraints excluded: chain A residue  889 ILE
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  903 ASN
Chi-restraints excluded: chain A residue 1040 ILE
Chi-restraints excluded: chain A residue 1125 ILE
Chi-restraints excluded: chain A residue 1169 PHE
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1239 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 73 optimal weight:    0.3980
   chunk 61 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 93 optimal weight:    8.9990
   chunk 121 optimal weight:    0.0050
   chunk 59 optimal weight:    0.2980
   chunk 107 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0270
   chunk 104 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.7454

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

Flipped N/Q/H residues before XYZ refinement:
** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 942 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 = 0.4155 r_free = 0.4155 target = 0.107613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.084664 restraints weight = 36064.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.087297 restraints weight = 20334.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.089052 restraints weight = 14070.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.5436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10194  Z= 0.116
  Angle     :  0.662  11.545  13812  Z= 0.332
  Chirality :  0.046   0.155   1536
  Planarity :  0.004   0.051   1793
  Dihedral  :  4.798  30.959   1333
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.88 %
    Favored  : 88.12 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 27.22 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.23), residues: 1229
  helix:  0.21 (0.30), residues: 329
  sheet: -2.03 (0.47), residues: 106
  loop : -2.93 (0.20), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1241 
 HIS   0.002   0.000   HIS A1041 
 PHE   0.017   0.001   PHE A 211 
 TYR   0.025   0.001   TYR A1180 
 ARG   0.004   0.000   ARG A 863 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03252 (  248)
  hydrogen bonds       : angle       4.39705 (  678)
  SS BOND              : bond        0.00783 (    1)
  SS BOND              : angle       2.44997 (    2)
  covalent geometry    : bond        0.00258 (10193)
  covalent geometry    : angle       0.66124 (13810)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3866.65 seconds
wall clock time: 68 minutes 46.50 seconds (4126.50 seconds total)