Starting phenix.real_space_refine
on Fri Feb 14 10:37:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qfp_13946/02_2025/7qfp_13946.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qfp_13946/02_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_13946/02_2025/7qfp_13946.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qfp_13946/02_2025/7qfp_13946.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qfp_13946/02_2025/7qfp_13946.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qfp_13946/02_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-5592/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: 6.03, per 1000 atoms: 0.60
  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: 2.47
  Conformation dependent library (CDL) restraints added in 1.1 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: 1.15
  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: 3.71

  Time building geometry restraints manager: 2.88 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:             1.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.140
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.510
-------------------------------------------------------------------------------
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  10193  Z= 0.418
  Angle     :  1.109  10.154  13810  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 

*********************** 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  : 1.165 
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: 0.2407
  time to fit residues: 83.2339
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  : 1.134 
-------------------------------------------------------------------------------
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 = 35)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.088155 restraints weight = 35321.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.090859 restraints weight = 19499.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.092711 restraints weight = 13211.702|
|-----------------------------------------------------------------------------|
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  10193  Z= 0.187
  Angle     :  0.669   7.699  13810  Z= 0.356
  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 

*********************** 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  : 1.055 
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: 0.5381 (mmm)
REVERT: A  158 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8163 (mm110)
REVERT: A  266 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8652 (mt)
REVERT: A  555 THR cc_start: 0.6951 (OUTLIER) cc_final: 0.6668 (t)
REVERT: A  578 ASN cc_start: 0.8976 (m110) cc_final: 0.8379 (p0)
REVERT: A  600 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8684 (m-80)
REVERT: A  637 ASN cc_start: 0.7785 (p0) cc_final: 0.7536 (p0)
REVERT: A  645 LEU cc_start: 0.7925 (mt) cc_final: 0.7648 (mt)
REVERT: A  689 LYS cc_start: 0.9172 (mmmm) cc_final: 0.8588 (pttt)
REVERT: A  758 LYS cc_start: 0.4571 (OUTLIER) cc_final: 0.4134 (pttm)
REVERT: A  870 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8159 (tt)
REVERT: A 1022 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7645 (tt)
REVERT: A 1044 ASP cc_start: 0.9176 (p0) cc_final: 0.8860 (p0)
REVERT: A 1076 ILE cc_start: 0.8232 (mm) cc_final: 0.8011 (mm)
REVERT: A 1163 ASP cc_start: 0.7076 (t0) cc_final: 0.6709 (t0)
  outliers start: 40
  outliers final: 17
  residues processed: 169
  average time/residue: 0.2176
  time to fit residues: 52.5265
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  : 1.097 
-------------------------------------------------------------------------------
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:    7.9990
   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:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 79 optimal weight:    8.9990
   chunk 122 optimal weight:    6.9990
   overall best weight:    4.7988

-------------------------------------------------------------------------------
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 = 0.4039 r_free = 0.4039 target = 0.100536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.078165 restraints weight = 37265.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.080553 restraints weight = 21311.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.082142 restraints weight = 14912.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.3987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.087  10193  Z= 0.438
  Angle     :  0.829  13.325  13810  Z= 0.440
  Chirality :  0.050   0.233   1536
  Planarity :  0.005   0.075   1793
  Dihedral  :  7.051  74.657   1350
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 19.15
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 15.13 %
    Favored  : 84.78 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 20.35 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.09 %
  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: -1.11 (0.26), residues: 337
  sheet: -2.46 (0.45), residues: 107
  loop : -3.38 (0.19), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A1241 
 HIS   0.004   0.001   HIS A  73 
 PHE   0.022   0.003   PHE A 209 
 TYR   0.025   0.002   TYR A 324 
 ARG   0.009   0.001   ARG A 863 

*********************** 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
  157 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 98
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6723 (mmm) cc_final: 0.6191 (mmm)
REVERT: A  123 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8365 (tm-30)
REVERT: A  324 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7347 (p90)
REVERT: A  460 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.6703 (m-80)
REVERT: A  645 LEU cc_start: 0.8076 (mt) cc_final: 0.7731 (mt)
REVERT: A  758 LYS cc_start: 0.4657 (OUTLIER) cc_final: 0.4409 (pttm)
REVERT: A  930 LYS cc_start: 0.8260 (tppt) cc_final: 0.8044 (tppt)
REVERT: A 1022 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8701 (tt)
REVERT: A 1044 ASP cc_start: 0.9168 (p0) cc_final: 0.8867 (p0)
REVERT: A 1070 GLU cc_start: 0.4663 (tp30) cc_final: 0.4254 (tp30)
REVERT: A 1077 GLN cc_start: 0.8575 (mp10) cc_final: 0.8331 (pm20)
REVERT: A 1163 ASP cc_start: 0.7431 (t0) cc_final: 0.6987 (t0)
REVERT: A 1207 MET cc_start: 0.5480 (OUTLIER) cc_final: 0.5077 (mtt)
REVERT: A 1241 TRP cc_start: 0.8248 (p-90) cc_final: 0.8041 (p-90)
  outliers start: 59
  outliers final: 30
  residues processed: 147
  average time/residue: 0.2329
  time to fit residues: 49.0214
Evaluate side-chains
  123 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 88
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 42 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 102 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 108 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9980
   chunk 110 optimal weight:   20.0000
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 903 ASN
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.104244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.081624 restraints weight = 36557.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.084140 restraints weight = 20682.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.085832 restraints weight = 14373.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.4089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10193  Z= 0.190
  Angle     :  0.647  13.493  13810  Z= 0.336
  Chirality :  0.045   0.162   1536
  Planarity :  0.004   0.053   1793
  Dihedral  :  6.382  77.442   1344
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.07 %
    Favored  : 88.85 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 22.11 %
    Favored  : 74.10 %
  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: -3.40 (0.22), residues: 1229
  helix: -0.44 (0.29), residues: 331
  sheet: -2.37 (0.45), residues: 105
  loop : -3.29 (0.19), residues: 793

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 978 
 HIS   0.002   0.000   HIS A 817 
 PHE   0.020   0.001   PHE A1114 
 TYR   0.019   0.001   TYR A1023 
 ARG   0.006   0.001   ARG A1062 

*********************** 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
  158 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 115
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.6687 (mmm) cc_final: 0.6271 (mmm)
REVERT: A  123 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8192 (tm-30)
REVERT: A  645 LEU cc_start: 0.7823 (mt) cc_final: 0.7544 (mt)
REVERT: A  981 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6806 (tm-30)
REVERT: A 1044 ASP cc_start: 0.9218 (p0) cc_final: 0.8995 (p0)
REVERT: A 1063 TYR cc_start: 0.7385 (m-80) cc_final: 0.7137 (m-80)
REVERT: A 1070 GLU cc_start: 0.4322 (tp30) cc_final: 0.4014 (tp30)
REVERT: A 1163 ASP cc_start: 0.7381 (t0) cc_final: 0.7034 (t0)
REVERT: A 1241 TRP cc_start: 0.8246 (p-90) cc_final: 0.7854 (p-90)
  outliers start: 43
  outliers final: 30
  residues processed: 148
  average time/residue: 0.2066
  time to fit residues: 44.2851
Evaluate side-chains
  131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 100
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
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  368 TYR
Chi-restraints excluded: chain A residue  386 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  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  661 THR
Chi-restraints excluded: chain A residue  690 GLU
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  917 ILE
Chi-restraints excluded: chain A residue  923 ILE
Chi-restraints excluded: chain A residue  932 PHE
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  981 GLN
Chi-restraints excluded: chain A residue 1040 ILE
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1125 ILE
Chi-restraints excluded: chain A residue 1138 LEU
Chi-restraints excluded: chain A residue 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:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 106 optimal weight:    9.9990
   chunk 6 optimal weight:    0.0470
   chunk 22 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.1280

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
A 158 GLN
A 217 ASN
** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 407 ASN
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.105596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.083388 restraints weight = 36332.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.087458 restraints weight = 20385.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.088567 restraints weight = 11316.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.4281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10193  Z= 0.174
  Angle     :  0.640  12.927  13810  Z= 0.326
  Chirality :  0.045   0.159   1536
  Planarity :  0.004   0.051   1793
  Dihedral  :  5.772  78.004   1338
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.96 %
    Favored  : 87.96 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 22.11 %
    Favored  : 73.39 %
  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: -3.15 (0.22), residues: 1229
  helix: -0.14 (0.29), residues: 329
  sheet: -2.25 (0.45), residues: 115
  loop : -3.16 (0.20), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1241 
 HIS   0.001   0.000   HIS A 817 
 PHE   0.019   0.001   PHE A 211 
 TYR   0.026   0.001   TYR A1180 
 ARG   0.004   0.000   ARG A 717 

*********************** 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
  162 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 111
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8161 (tm-30)
REVERT: A  460 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.6219 (m-80)
REVERT: A  600 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8531 (m-80)
REVERT: A  645 LEU cc_start: 0.7827 (mt) cc_final: 0.7529 (mt)
REVERT: A  741 ASN cc_start: 0.9368 (m-40) cc_final: 0.8812 (p0)
REVERT: A  870 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7991 (mm)
REVERT: A 1044 ASP cc_start: 0.9192 (p0) cc_final: 0.8962 (p0)
REVERT: A 1063 TYR cc_start: 0.7342 (m-80) cc_final: 0.7107 (m-80)
REVERT: A 1070 GLU cc_start: 0.4520 (tp30) cc_final: 0.4083 (tp30)
REVERT: A 1163 ASP cc_start: 0.7445 (t0) cc_final: 0.7149 (t0)
REVERT: A 1241 TRP cc_start: 0.8418 (p-90) cc_final: 0.8091 (p-90)
  outliers start: 51
  outliers final: 34
  residues processed: 148
  average time/residue: 0.2092
  time to fit residues: 45.2667
Evaluate side-chains
  135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 98
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
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  430 LYS
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  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  661 THR
Chi-restraints excluded: chain A residue  690 GLU
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  889 ILE
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 1125 ILE
Chi-restraints excluded: chain A residue 1138 LEU
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:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   chunk 69 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 30 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 103 optimal weight:    0.2980
   chunk 111 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 76 optimal weight:    0.0570
   overall best weight:    1.2102

-------------------------------------------------------------------------------
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 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1107 ASN ** 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 = 0.4128 r_free = 0.4128 target = 0.105685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.082953 restraints weight = 36200.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.085519 restraints weight = 20272.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.087246 restraints weight = 13968.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.4464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10193  Z= 0.174
  Angle     :  0.634  12.213  13810  Z= 0.323
  Chirality :  0.045   0.155   1536
  Planarity :  0.003   0.049   1793
  Dihedral  :  5.730  83.985   1338
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.23 %
    Favored  : 88.69 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 23.17 %
    Favored  : 72.60 %
  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: -0.00 (0.30), residues: 329
  sheet: -2.27 (0.45), residues: 115
  loop : -3.11 (0.20), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 937 
 HIS   0.001   0.000   HIS A 817 
 PHE   0.018   0.001   PHE A 211 
 TYR   0.015   0.001   TYR A1023 
 ARG   0.003   0.000   ARG A 863 

*********************** 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
  153 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 105
  time to evaluate  : 1.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8232 (tm-30)
REVERT: A  460 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.6220 (m-80)
REVERT: A  600 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8522 (m-80)
REVERT: A  645 LEU cc_start: 0.7813 (mt) cc_final: 0.7511 (mt)
REVERT: A  741 ASN cc_start: 0.9341 (m-40) cc_final: 0.8787 (p0)
REVERT: A  788 MET cc_start: 0.8630 (mmm) cc_final: 0.8368 (mmm)
REVERT: A  870 LEU cc_start: 0.8654 (tt) cc_final: 0.8099 (mm)
REVERT: A  903 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8060 (t0)
REVERT: A  930 LYS cc_start: 0.7561 (tppt) cc_final: 0.7297 (tppt)
REVERT: A 1044 ASP cc_start: 0.9212 (p0) cc_final: 0.8985 (p0)
REVERT: A 1063 TYR cc_start: 0.7376 (m-80) cc_final: 0.7123 (m-80)
REVERT: A 1070 GLU cc_start: 0.4670 (tp30) cc_final: 0.4334 (tp30)
REVERT: A 1163 ASP cc_start: 0.7458 (t0) cc_final: 0.7122 (t0)
REVERT: A 1216 MET cc_start: 0.3567 (mmm) cc_final: 0.3361 (mmt)
REVERT: A 1241 TRP cc_start: 0.8425 (p-90) cc_final: 0.8075 (p-90)
  outliers start: 48
  outliers final: 37
  residues processed: 143
  average time/residue: 0.2122
  time to fit residues: 44.3055
Evaluate side-chains
  141 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 101
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
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  247 LYS
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  298 LYS
Chi-restraints excluded: chain A residue  351 PHE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  386 TYR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  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  727 ASN
Chi-restraints excluded: chain A residue  834 ASP
Chi-restraints excluded: chain A residue  868 SER
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  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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 109 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 122 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 41 optimal weight:    8.9990
   chunk 56 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1107 ASN ** 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 = 0.4156 r_free = 0.4156 target = 0.107332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.084368 restraints weight = 36300.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.087019 restraints weight = 20480.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.088789 restraints weight = 14159.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.4585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  10193  Z= 0.156
  Angle     :  0.619  11.344  13810  Z= 0.313
  Chirality :  0.045   0.158   1536
  Planarity :  0.003   0.049   1793
  Dihedral  :  5.616  89.040   1338
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.82 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 23.44 %
    Favored  : 72.78 %
  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:  0.25 (0.31), residues: 323
  sheet: -2.19 (0.45), residues: 120
  loop : -3.03 (0.20), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1241 
 HIS   0.002   0.000   HIS A1175 
 PHE   0.018   0.001   PHE A 211 
 TYR   0.026   0.001   TYR A1180 
 ARG   0.002   0.000   ARG A1016 

*********************** 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
  154 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 111
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8502 (tm-30)
REVERT: A  460 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.6245 (m-80)
REVERT: A  600 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8496 (m-80)
REVERT: A  645 LEU cc_start: 0.7889 (mt) cc_final: 0.7546 (mt)
REVERT: A  741 ASN cc_start: 0.9274 (m-40) cc_final: 0.8678 (p0)
REVERT: A  788 MET cc_start: 0.8554 (mmm) cc_final: 0.8081 (mmm)
REVERT: A  868 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.8156 (p)
REVERT: A  870 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8028 (mm)
REVERT: A  903 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8086 (t0)
REVERT: A 1044 ASP cc_start: 0.9222 (p0) cc_final: 0.8996 (p0)
REVERT: A 1063 TYR cc_start: 0.7348 (m-80) cc_final: 0.7056 (m-80)
REVERT: A 1070 GLU cc_start: 0.4625 (tp30) cc_final: 0.4229 (tp30)
REVERT: A 1163 ASP cc_start: 0.7468 (t0) cc_final: 0.7086 (t0)
REVERT: A 1241 TRP cc_start: 0.8373 (p-90) cc_final: 0.7981 (p-90)
  outliers start: 43
  outliers final: 30
  residues processed: 145
  average time/residue: 0.2376
  time to fit residues: 49.9669
Evaluate side-chains
  137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 102
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
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  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  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  727 ASN
Chi-restraints excluded: chain A residue  868 SER
Chi-restraints excluded: chain A residue  870 LEU
Chi-restraints excluded: chain A residue  889 ILE
Chi-restraints excluded: chain A residue  900 THR
Chi-restraints excluded: chain A residue  903 ASN
Chi-restraints excluded: chain A residue  932 PHE
Chi-restraints excluded: chain A residue  935 SER
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 40 optimal weight:    9.9990
   chunk 62 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 114 optimal weight:    5.9990
   chunk 82 optimal weight:    0.4980
   overall best weight:    2.0786

-------------------------------------------------------------------------------
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 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 792 ASN
A 829 ASN
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 983 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.104864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.081742 restraints weight = 36403.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.084299 restraints weight = 20703.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.085985 restraints weight = 14420.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.4923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10193  Z= 0.224
  Angle     :  0.649  11.090  13810  Z= 0.334
  Chirality :  0.046   0.166   1536
  Planarity :  0.004   0.045   1793
  Dihedral  :  5.723  94.432   1336
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.77 %
    Favored  : 87.23 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 24.32 %
    Favored  : 71.63 %
  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: -2.97 (0.23), residues: 1229
  helix:  0.07 (0.30), residues: 333
  sheet: -2.11 (0.45), residues: 120
  loop : -3.09 (0.20), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1241 
 HIS   0.003   0.001   HIS A1264 
 PHE   0.021   0.002   PHE A 571 
 TYR   0.021   0.001   TYR A 743 
 ARG   0.004   0.000   ARG A 863 

*********************** 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
  149 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 103
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8236 (tm-30)
REVERT: A  460 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.6428 (m-80)
REVERT: A  645 LEU cc_start: 0.7909 (mt) cc_final: 0.7554 (mt)
REVERT: A  741 ASN cc_start: 0.9343 (m-40) cc_final: 0.8758 (p0)
REVERT: A  903 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8155 (t0)
REVERT: A  938 VAL cc_start: 0.9200 (t) cc_final: 0.8976 (m)
REVERT: A 1044 ASP cc_start: 0.9220 (p0) cc_final: 0.9013 (p0)
REVERT: A 1063 TYR cc_start: 0.7461 (m-80) cc_final: 0.7212 (m-80)
REVERT: A 1163 ASP cc_start: 0.7544 (t0) cc_final: 0.7173 (t0)
REVERT: A 1241 TRP cc_start: 0.8379 (p-90) cc_final: 0.7958 (p-90)
  outliers start: 46
  outliers final: 36
  residues processed: 142
  average time/residue: 0.2022
  time to fit residues: 42.4281
Evaluate side-chains
  135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 97
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
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  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  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  727 ASN
Chi-restraints excluded: chain A residue  868 SER
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  956 ILE
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 1228 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:   10.0000
   chunk 67 optimal weight:    6.9990
   chunk 71 optimal weight:    9.9990
   chunk 45 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
A 447 ASN
** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 892 ASN
A 904 GLN
** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1203 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.100847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.078268 restraints weight = 37106.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.080606 restraints weight = 21874.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.082194 restraints weight = 15505.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.5424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  10193  Z= 0.360
  Angle     :  0.759  10.873  13810  Z= 0.397
  Chirality :  0.049   0.156   1536
  Planarity :  0.004   0.047   1793
  Dihedral  :  6.211  91.613   1336
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 15.62 %
    Favored  : 84.30 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 24.14 %
    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: -3.38 (0.22), residues: 1229
  helix: -0.47 (0.28), residues: 335
  sheet: -2.07 (0.51), residues: 95
  loop : -3.31 (0.19), residues: 799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A1257 
 HIS   0.003   0.001   HIS A  73 
 PHE   0.021   0.002   PHE A1048 
 TYR   0.029   0.002   TYR A1180 
 ARG   0.007   0.001   ARG A 863 

*********************** 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
  148 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 101
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8216 (tm-30)
REVERT: A  216 MET cc_start: 0.8065 (ptp) cc_final: 0.7781 (ptp)
REVERT: A  460 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.6699 (m-80)
REVERT: A  645 LEU cc_start: 0.7899 (mt) cc_final: 0.7547 (mt)
REVERT: A  741 ASN cc_start: 0.9401 (m-40) cc_final: 0.8836 (p0)
REVERT: A  898 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8541 (m-10)
REVERT: A  903 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8198 (t0)
REVERT: A  946 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8867 (tptp)
REVERT: A 1063 TYR cc_start: 0.7394 (m-80) cc_final: 0.7097 (m-80)
REVERT: A 1163 ASP cc_start: 0.7567 (t0) cc_final: 0.7290 (t0)
REVERT: A 1241 TRP cc_start: 0.8253 (p-90) cc_final: 0.7808 (p-90)
  outliers start: 47
  outliers final: 38
  residues processed: 140
  average time/residue: 0.2297
  time to fit residues: 46.6886
Evaluate side-chains
  136 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 94
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
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  293 LEU
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  447 ASN
Chi-restraints excluded: chain A residue  460 TYR
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  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  727 ASN
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  787 LEU
Chi-restraints excluded: chain A residue  868 SER
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  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 1228 LEU
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:    0.6980
   chunk 59 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 109 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0670
   chunk 106 optimal weight:    4.9990
   overall best weight:    1.2922

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

Flipped N/Q/H residues before XYZ refinement:
** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 892 ASN
A1203 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.104351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.081354 restraints weight = 35993.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.083878 restraints weight = 20473.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.085547 restraints weight = 14235.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.5446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10193  Z= 0.195
  Angle     :  0.713  11.251  13810  Z= 0.361
  Chirality :  0.047   0.197   1536
  Planarity :  0.004   0.051   1793
  Dihedral  :  5.960  94.291   1336
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.69 %
    Favored  : 87.31 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 25.46 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.17 (0.22), residues: 1229
  helix: -0.26 (0.29), residues: 336
  sheet: -2.15 (0.51), residues: 94
  loop : -3.16 (0.20), residues: 799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1241 
 HIS   0.001   0.000   HIS A 817 
 PHE   0.019   0.002   PHE A1048 
 TYR   0.028   0.001   TYR A 743 
 ARG   0.003   0.000   ARG A 863 

********************** 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
  136 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 1.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8220 (tm-30)
REVERT: A  460 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.6406 (m-80)
REVERT: A  645 LEU cc_start: 0.7901 (mt) cc_final: 0.7550 (mt)
REVERT: A  741 ASN cc_start: 0.9379 (m-40) cc_final: 0.8785 (p0)
REVERT: A  903 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8102 (t0)
REVERT: A  928 LYS cc_start: 0.8075 (pttm) cc_final: 0.7816 (ptpp)
REVERT: A 1063 TYR cc_start: 0.7267 (m-80) cc_final: 0.7035 (m-80)
REVERT: A 1163 ASP cc_start: 0.7567 (t0) cc_final: 0.7173 (t0)
REVERT: A 1241 TRP cc_start: 0.8231 (p-90) cc_final: 0.7797 (p-90)
REVERT: A 1257 TRP cc_start: 0.5957 (m100) cc_final: 0.5652 (m100)
  outliers start: 36
  outliers final: 34
  residues processed: 132
  average time/residue: 0.2194
  time to fit residues: 42.8342
Evaluate side-chains
  128 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 92
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
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  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  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  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  727 ASN
Chi-restraints excluded: chain A residue  868 SER
Chi-restraints excluded: chain A residue  892 ASN
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  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 1228 LEU
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:    0.6980
   chunk 61 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 121 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0870
   chunk 63 optimal weight:    8.9990
   chunk 104 optimal weight:    0.8980
   chunk 23 optimal weight:    8.9990
   overall best weight:    0.9360

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

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 892 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.104455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.081360 restraints weight = 36136.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.083911 restraints weight = 20516.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.085567 restraints weight = 14280.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.5467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.139  10193  Z= 0.251
  Angle     :  0.967  59.198  13810  Z= 0.546
  Chirality :  0.048   0.347   1536
  Planarity :  0.004   0.052   1793
  Dihedral  :  6.007  94.325   1336
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.37 %
    Favored  : 87.63 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 25.55 %
    Favored  : 70.84 %
  Cbeta Deviations :  0.09 %
  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: -3.18 (0.22), residues: 1229
  helix: -0.26 (0.29), residues: 336
  sheet: -2.21 (0.51), residues: 94
  loop : -3.15 (0.20), residues: 799

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   0.028   0.002   PHE A 857 
 TYR   0.027   0.001   TYR A 743 
 ARG   0.013   0.000   ARG A 863 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3550.91 seconds
wall clock time: 64 minutes 41.22 seconds (3881.22 seconds total)