Starting phenix.real_space_refine
on Sat Jul 26 17:31:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nfi_49366/07_2025/9nfi_49366_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nfi_49366/07_2025/9nfi_49366.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nfi_49366/07_2025/9nfi_49366.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nfi_49366/07_2025/9nfi_49366.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nfi_49366/07_2025/9nfi_49366_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nfi_49366/07_2025/9nfi_49366_neut.cif"
  }
  resolution = 3.79
  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=   0.000 sd=   0.044
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      49      5.16       5
     C    5550      2.51       5
     N    1468      2.21       5
     O    1597      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8664
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8664
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1116, 8664
          Classifications: {'peptide': 1116}
          Link IDs: {'PTRANS': 32, 'TRANS': 1083}
          Chain breaks: 5
  Time building chain proxies: 4.88, per 1000 atoms: 0.56
  Number of scatterers: 8664
  At special positions: 0
  Unit cell: (82.28, 99.11, 142.12, 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      49     16.00
     O    1597      8.00
     N    1468      7.00
     C    5550      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.27
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2064

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      65.9% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 52
      removed outlier: 3.592A  pdb=" N   PHE A  52 " --> pdb=" O   LEU A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 96
      Proline residue:  A  78  - end of helix
      removed outlier: 4.166A  pdb=" N   CYS A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   MET A  96 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 170
    Processing helix  chain 'A' and resid 171 through 177
      removed outlier: 3.908A  pdb=" N   PHE A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 222
      removed outlier: 3.974A  pdb=" N   ASP A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   LYS A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   VAL A 202 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLY A 203 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 232
    Processing helix  chain 'A' and resid 256 through 272
      removed outlier: 5.515A  pdb=" N   LYS A 261 " --> pdb=" O   THR A 257 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   ALA A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 279
    Processing helix  chain 'A' and resid 281 through 336
    Processing helix  chain 'A' and resid 341 through 382
      removed outlier: 4.192A  pdb=" N   SER A 361 " --> pdb=" O   MET A 357 " (cutoff:3.500A)
      Proline residue:  A 362  - end of helix
    Processing helix  chain 'A' and resid 445 through 453
      removed outlier: 4.130A  pdb=" N   ILE A 449 " --> pdb=" O   LYS A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 481
    Processing helix  chain 'A' and resid 495 through 502
      removed outlier: 3.551A  pdb=" N   TYR A 502 " --> pdb=" O   GLU A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 520
    Processing helix  chain 'A' and resid 544 through 559
      removed outlier: 4.122A  pdb=" N   ARG A 559 " --> pdb=" O   ARG A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 589
      removed outlier: 4.101A  pdb=" N   ILE A 580 " --> pdb=" O   GLU A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 630
      removed outlier: 3.584A  pdb=" N   LYS A 630 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 716 through 723
    Processing helix  chain 'A' and resid 725 through 756
      Proline residue:  A 744  - end of helix
    Processing helix  chain 'A' and resid 762 through 816
    Processing helix  chain 'A' and resid 818 through 823
      removed outlier: 3.743A  pdb=" N   ASP A 822 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ASN A 823 " --> pdb=" O   GLY A 819 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 818 through 823'
    Processing helix  chain 'A' and resid 824 through 826
      No H-bonds generated for 'chain 'A' and resid 824 through 826'
    Processing helix  chain 'A' and resid 827 through 871
      removed outlier: 4.429A  pdb=" N   ALA A 839 " --> pdb=" O   LEU A 835 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   ALA A 840 " --> pdb=" O   ALA A 836 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   GLY A 847 " --> pdb=" O   GLN A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 871 through 880
    Processing helix  chain 'A' and resid 883 through 891
      removed outlier: 4.322A  pdb=" N   VAL A 887 " --> pdb=" O   PRO A 883 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA A 888 " --> pdb=" O   ILE A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 903 through 920
      removed outlier: 3.761A  pdb=" N   ALA A 910 " --> pdb=" O   GLU A 906 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ILE A 913 " --> pdb=" O   LYS A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 927
    Processing helix  chain 'A' and resid 929 through 984
      removed outlier: 4.156A  pdb=" N   VAL A 943 " --> pdb=" O   GLU A 939 " (cutoff:3.500A)
      Proline residue:  A 944  - end of helix
      removed outlier: 3.975A  pdb=" N   ILE A 966 " --> pdb=" O   SER A 962 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   TYR A 967 " --> pdb=" O   GLN A 963 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   PHE A 974 " --> pdb=" O   TYR A 970 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ARG A 975 " --> pdb=" O   ALA A 971 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   PHE A 976 " --> pdb=" O   GLY A 972 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   TRP A 979 " --> pdb=" O   ARG A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 989 through 1002
    Processing helix  chain 'A' and resid 1014 through 1029
    Processing helix  chain 'A' and resid 1094 through 1101
    Processing helix  chain 'A' and resid 1122 through 1129
    Processing helix  chain 'A' and resid 1143 through 1150
    Processing helix  chain 'A' and resid 1158 through 1168
      removed outlier: 3.859A  pdb=" N   ILE A1162 " --> pdb=" O   THR A1158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1171 through 1176
    Processing helix  chain 'A' and resid 1180 through 1184
      removed outlier: 3.669A  pdb=" N   ASP A1183 " --> pdb=" O   GLN A1180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1194 through 1208
    Processing helix  chain 'A' and resid 1224 through 1239
      removed outlier: 4.370A  pdb=" N   LYS A1229 " --> pdb=" O   THR A1225 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   VAL A1230 " --> pdb=" O   GLU A1226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1256
      removed outlier: 4.012A  pdb=" N   ILE A1254 " --> pdb=" O   ARG A1250 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ASN A1256 " --> pdb=" O   SER A1252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1273 through 1280
    Processing helix  chain 'A' and resid 1282 through 1288
      removed outlier: 4.209A  pdb=" N   MET A1286 " --> pdb=" O   GLY A1282 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 429
      removed outlier: 5.394A  pdb=" N   ASN A 423 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   PHE A 411 " --> pdb=" O   ASN A 423 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   LEU A 427 " --> pdb=" O   ARG A 407 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   ARG A 407 " --> pdb=" O   LEU A 427 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   VAL A 429 " --> pdb=" O   GLU A 405 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   GLU A 405 " --> pdb=" O   VAL A 429 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   ILE A 409 " --> pdb=" O   GLU A 460 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   GLU A 460 " --> pdb=" O   ILE A 409 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 482 through 486
      removed outlier: 3.586A  pdb=" N   VAL A 596 " --> pdb=" O   ILE A 435 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ALA A 436 " --> pdb=" O   ALA A 611 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   PHE A 613 " --> pdb=" O   ALA A 436 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   VAL A 438 " --> pdb=" O   PHE A 613 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   ILE A 610 " --> pdb=" O   LEU A 621 " (cutoff:3.500A)
      removed outlier: 5.557A  pdb=" N   LEU A 621 " --> pdb=" O   ILE A 610 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLY A 612 " --> pdb=" O   ILE A 619 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1076 through 1077
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1130 through 1133
      removed outlier: 6.113A  pdb=" N   GLY A1131 " --> pdb=" O   LEU A1215 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU A1083 " --> pdb=" O   CYS A1244 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL A1246 " --> pdb=" O   LEU A1083 " (cutoff:3.500A)
      removed outlier: 5.801A  pdb=" N   THR A1082 " --> pdb=" O   ARG A1259 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1263 through 1264

    554 hydrogen bonds defined for protein.
    1632 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: 2.87

  Time building geometry restraints manager: 2.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2820
        1.34 -     1.46: 1671
        1.46 -     1.58: 4240
        1.58 -     1.69: 0
        1.69 -     1.81: 89
  Bond restraints: 8820
  Sorted by residual:
  bond pdb=" C   ALA A  50 "
       pdb=" N   LEU A  51 "
    ideal  model  delta    sigma   weight residual
    1.332  1.308  0.025 1.40e-02 5.10e+03 3.07e+00
  bond pdb=" CB  GLN A 542 "
       pdb=" CG  GLN A 542 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.17e+00
  bond pdb=" CA  GLU A1101 "
       pdb=" C   GLU A1101 "
    ideal  model  delta    sigma   weight residual
    1.522  1.504  0.018 1.72e-02 3.38e+03 1.06e+00
  bond pdb=" CA  GLN A 743 "
       pdb=" C   GLN A 743 "
    ideal  model  delta    sigma   weight residual
    1.521  1.533 -0.011 1.17e-02 7.31e+03 9.15e-01
  bond pdb=" C   GLU A 902 "
       pdb=" O   GLU A 902 "
    ideal  model  delta    sigma   weight residual
    1.231  1.250 -0.019 2.00e-02 2.50e+03 8.64e-01
  ... (remaining 8815 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 11811
        2.56 -     5.13: 89
        5.13 -     7.69: 8
        7.69 -    10.26: 2
       10.26 -    12.82: 1
  Bond angle restraints: 11911
  Sorted by residual:
  angle pdb=" C   TRP A 224 "
        pdb=" N   LYS A 225 "
        pdb=" CA  LYS A 225 "
      ideal   model   delta    sigma   weight residual
     122.40  135.22  -12.82 1.45e+00 4.76e-01 7.82e+01
  angle pdb=" C   THR A 846 "
        pdb=" N   GLY A 847 "
        pdb=" CA  GLY A 847 "
      ideal   model   delta    sigma   weight residual
     120.00  127.21   -7.21 1.10e+00 8.26e-01 4.30e+01
  angle pdb=" CA  MET A 885 "
        pdb=" CB  MET A 885 "
        pdb=" CG  MET A 885 "
      ideal   model   delta    sigma   weight residual
     114.10  121.44   -7.34 2.00e+00 2.50e-01 1.35e+01
  angle pdb=" CB  MET A 168 "
        pdb=" CG  MET A 168 "
        pdb=" SD  MET A 168 "
      ideal   model   delta    sigma   weight residual
     112.70  121.50   -8.80 3.00e+00 1.11e-01 8.61e+00
  angle pdb=" N   VAL A 891 "
        pdb=" CA  VAL A 891 "
        pdb=" C   VAL A 891 "
      ideal   model   delta    sigma   weight residual
     112.98  109.36    3.62 1.25e+00 6.40e-01 8.38e+00
  ... (remaining 11906 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 4600
       17.83 -    35.67: 535
       35.67 -    53.50: 124
       53.50 -    71.34: 17
       71.34 -    89.17: 14
  Dihedral angle restraints: 5290
    sinusoidal: 2083
      harmonic: 3207
  Sorted by residual:
  dihedral pdb=" CA  GLU A 902 "
           pdb=" C   GLU A 902 "
           pdb=" N   ASP A 903 "
           pdb=" CA  ASP A 903 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.81   22.19     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  PRO A 883 "
           pdb=" C   PRO A 883 "
           pdb=" N   ILE A 884 "
           pdb=" CA  ILE A 884 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.10   21.90     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  GLN A1271 "
           pdb=" C   GLN A1271 "
           pdb=" N   GLY A1272 "
           pdb=" CA  GLY A1272 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.24  -18.76     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 5287 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1266
       0.072 -    0.144: 98
       0.144 -    0.216: 1
       0.216 -    0.289: 0
       0.289 -    0.361: 2
  Chirality restraints: 1367
  Sorted by residual:
  chirality pdb=" CA  PHE A 976 "
            pdb=" N   PHE A 976 "
            pdb=" C   PHE A 976 "
            pdb=" CB  PHE A 976 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.25e+00
  chirality pdb=" CA  ARG A 975 "
            pdb=" N   ARG A 975 "
            pdb=" C   ARG A 975 "
            pdb=" CB  ARG A 975 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.69e+00
  chirality pdb=" CB  ILE A 753 "
            pdb=" CA  ILE A 753 "
            pdb=" CG1 ILE A 753 "
            pdb=" CG2 ILE A 753 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.96e-01
  ... (remaining 1364 not shown)

  Planarity restraints: 1517
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  77 "   -0.043 5.00e-02 4.00e+02   6.47e-02 6.70e+00
        pdb=" N   PRO A  78 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A  78 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A  78 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A1074 "    0.008 2.00e-02 2.50e+03   1.55e-02 2.39e+00
        pdb=" C   ASN A1074 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ASN A1074 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A1075 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 560 "    0.025 5.00e-02 4.00e+02   3.83e-02 2.35e+00
        pdb=" N   PRO A 561 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 561 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 561 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1514 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 154
        2.62 -     3.19: 8824
        3.19 -     3.76: 13801
        3.76 -     4.33: 17644
        4.33 -     4.90: 29316
  Nonbonded interactions: 69739
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 872 "
            pdb=" OG1 THR A 875 "
     model   vdw
     2.046 3.040
  nonbonded pdb=" ND2 ASN A 184 "
            pdb=" OG1 THR A 915 "
     model   vdw
     2.091 3.120
  nonbonded pdb=" O   TRP A 820 "
            pdb=" ND2 ASN A 826 "
     model   vdw
     2.099 3.120
  nonbonded pdb=" OG  SER A 724 "
            pdb=" OE1 GLU A 725 "
     model   vdw
     2.100 3.040
  nonbonded pdb=" OG  SER A 335 "
            pdb=" OE2 GLU A 337 "
     model   vdw
     2.100 3.040
  ... (remaining 69734 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:             0.300
  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:                     22.250
  Find NCS groups from input model:        0.090
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8820  Z= 0.151
  Angle     :  0.620  12.819  11911  Z= 0.346
  Chirality :  0.039   0.361   1367
  Planarity :  0.004   0.065   1517
  Dihedral  : 16.380  89.171   3226
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 19.09 %
    Favored  : 79.72 %
  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:  0.44 (0.25), residues: 1104
  helix:  1.58 (0.19), residues: 680
  sheet: -0.73 (0.66), residues: 59
  loop : -2.12 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1125 
 HIS   0.005   0.001   HIS A 375 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.014   0.001   TYR A 322 
 ARG   0.005   0.000   ARG A 407 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10929 (  554)
  hydrogen bonds       : angle       4.86920 ( 1632)
  covalent geometry    : bond        0.00319 ( 8820)
  covalent geometry    : angle       0.61953 (11911)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 171
  time to evaluate  : 0.913 
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   64 PHE cc_start: 0.7570 (m-10) cc_final: 0.7287 (t80)
REVERT: A   80 MET cc_start: 0.7381 (tpt) cc_final: 0.5341 (ptt)
REVERT: A  135 PHE cc_start: 0.7921 (t80) cc_final: 0.7653 (t80)
REVERT: A  143 MET cc_start: 0.8031 (mtm) cc_final: 0.7709 (mtp)
REVERT: A  168 MET cc_start: 0.9012 (mmm) cc_final: 0.8310 (mmm)
REVERT: A  174 TRP cc_start: 0.8604 (t60) cc_final: 0.8319 (t60)
REVERT: A  267 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6967 (tp30)
REVERT: A  334 MET cc_start: 0.5235 (mmt) cc_final: 0.4167 (ttt)
REVERT: A  723 LEU cc_start: 0.8944 (mt) cc_final: 0.8550 (tt)
REVERT: A  734 PHE cc_start: 0.7612 (t80) cc_final: 0.7143 (t80)
REVERT: A  737 ILE cc_start: 0.8509 (mm) cc_final: 0.8230 (tt)
REVERT: A  742 MET cc_start: 0.6933 (tpt) cc_final: 0.6337 (mtm)
REVERT: A  873 GLU cc_start: 0.8455 (mp0) cc_final: 0.8035 (mt-10)
REVERT: A  939 GLU cc_start: 0.8199 (tp30) cc_final: 0.7953 (tm-30)
REVERT: A 1047 LYS cc_start: 0.8021 (tmtt) cc_final: 0.7671 (tptt)
REVERT: A 1101 GLU cc_start: 0.8732 (mm-30) cc_final: 0.7885 (tp30)
  outliers start: 11
  outliers final: 4
  residues processed: 178
  average time/residue: 0.2020
  time to fit residues: 50.1676
Evaluate side-chains
  140 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 136
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  892 GLN
Chi-restraints excluded: chain A residue 1081 GLU
Chi-restraints excluded: chain A residue 1114 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    9.9990
   chunk 84 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   chunk 33 optimal weight:    7.9990
   chunk 52 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 ASN
A 292 ASN
A 423 ASN
A 547 GLN
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 892 GLN
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.137312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.117891 restraints weight = 22995.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.121058 restraints weight = 13023.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.123220 restraints weight = 8965.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8820  Z= 0.196
  Angle     :  0.657  13.716  11911  Z= 0.345
  Chirality :  0.041   0.179   1367
  Planarity :  0.004   0.045   1517
  Dihedral  :  4.931  40.590   1203
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.23 %
    Favored  : 78.53 %
  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:  0.41 (0.25), residues: 1104
  helix:  1.47 (0.19), residues: 677
  sheet: -0.54 (0.67), residues: 63
  loop : -1.94 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A1125 
 HIS   0.005   0.001   HIS A 375 
 PHE   0.018   0.002   PHE A 715 
 TYR   0.021   0.002   TYR A 289 
 ARG   0.005   0.001   ARG A1240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04419 (  554)
  hydrogen bonds       : angle       4.49830 ( 1632)
  covalent geometry    : bond        0.00439 ( 8820)
  covalent geometry    : angle       0.65707 (11911)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 154
  time to evaluate  : 0.925 
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   64 PHE cc_start: 0.7797 (m-10) cc_final: 0.7266 (t80)
REVERT: A   80 MET cc_start: 0.6790 (tpt) cc_final: 0.5822 (ptt)
REVERT: A  123 MET cc_start: 0.6699 (mmm) cc_final: 0.6440 (mmm)
REVERT: A  130 TYR cc_start: 0.5568 (m-80) cc_final: 0.5107 (m-80)
REVERT: A  142 TYR cc_start: 0.8765 (t80) cc_final: 0.8163 (t80)
REVERT: A  143 MET cc_start: 0.8042 (mtm) cc_final: 0.7694 (mtp)
REVERT: A  168 MET cc_start: 0.9311 (mmm) cc_final: 0.8563 (mmm)
REVERT: A  267 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7586 (tp30)
REVERT: A  293 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8475 (mm)
REVERT: A  334 MET cc_start: 0.4892 (mmt) cc_final: 0.4196 (ttp)
REVERT: A  378 TYR cc_start: 0.8423 (m-10) cc_final: 0.8205 (m-80)
REVERT: A  496 ILE cc_start: 0.5977 (OUTLIER) cc_final: 0.5775 (mp)
REVERT: A  500 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8918 (tt)
REVERT: A  637 LEU cc_start: 0.8035 (pp) cc_final: 0.7331 (mm)
REVERT: A  723 LEU cc_start: 0.8942 (mt) cc_final: 0.8558 (tt)
REVERT: A  734 PHE cc_start: 0.8062 (t80) cc_final: 0.7405 (t80)
REVERT: A  737 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8251 (tt)
REVERT: A  742 MET cc_start: 0.6267 (tpt) cc_final: 0.5917 (mtm)
REVERT: A  790 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7459 (tm-30)
REVERT: A  814 MET cc_start: 0.8140 (mmp) cc_final: 0.7784 (mmp)
REVERT: A  873 GLU cc_start: 0.8774 (mp0) cc_final: 0.8429 (mt-10)
REVERT: A  909 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.7897 (tppt)
REVERT: A  912 LYS cc_start: 0.8675 (tppt) cc_final: 0.8463 (ptpt)
REVERT: A  939 GLU cc_start: 0.8541 (tp30) cc_final: 0.8112 (tm-30)
REVERT: A  986 MET cc_start: 0.5270 (ppp) cc_final: 0.4920 (ppp)
REVERT: A  992 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.4213 (m-80)
REVERT: A 1020 MET cc_start: 0.8591 (tpt) cc_final: 0.8357 (tpt)
REVERT: A 1047 LYS cc_start: 0.8075 (tmtt) cc_final: 0.7769 (tptt)
REVERT: A 1074 ASN cc_start: 0.7674 (m-40) cc_final: 0.7400 (t0)
REVERT: A 1077 VAL cc_start: 0.6008 (OUTLIER) cc_final: 0.5711 (m)
REVERT: A 1101 GLU cc_start: 0.9420 (mm-30) cc_final: 0.7790 (tp30)
  outliers start: 30
  outliers final: 16
  residues processed: 172
  average time/residue: 0.1790
  time to fit residues: 44.8141
Evaluate side-chains
  158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  613 PHE
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  790 GLN
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain A residue  908 GLU
Chi-restraints excluded: chain A residue  909 LYS
Chi-restraints excluded: chain A residue  992 TYR
Chi-restraints excluded: chain A residue 1051 ASN
Chi-restraints excluded: chain A residue 1071 ARG
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1244 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 36 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 109 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 ASN
A 195 GLN
A 410 HIS
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 920 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.139474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.119564 restraints weight = 23342.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.122917 restraints weight = 13136.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.125142 restraints weight = 8969.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8820  Z= 0.135
  Angle     :  0.587  11.201  11911  Z= 0.305
  Chirality :  0.039   0.206   1367
  Planarity :  0.003   0.040   1517
  Dihedral  :  4.173  28.790   1195
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.50 %
    Favored  : 76.70 %
  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:  0.55 (0.25), residues: 1104
  helix:  1.55 (0.20), residues: 680
  sheet: -0.51 (0.67), residues: 63
  loop : -1.82 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A1125 
 HIS   0.006   0.001   HIS A 375 
 PHE   0.014   0.001   PHE A 715 
 TYR   0.018   0.001   TYR A 130 
 ARG   0.004   0.000   ARG A1240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03927 (  554)
  hydrogen bonds       : angle       4.19227 ( 1632)
  covalent geometry    : bond        0.00300 ( 8820)
  covalent geometry    : angle       0.58720 (11911)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 1.057 
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   64 PHE cc_start: 0.7740 (m-10) cc_final: 0.7311 (t80)
REVERT: A  142 TYR cc_start: 0.8801 (t80) cc_final: 0.8215 (t80)
REVERT: A  168 MET cc_start: 0.9371 (mmm) cc_final: 0.8818 (mmm)
REVERT: A  267 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7355 (tp30)
REVERT: A  334 MET cc_start: 0.4804 (mmt) cc_final: 0.4146 (ttm)
REVERT: A  355 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6397 (m-80)
REVERT: A  637 LEU cc_start: 0.7837 (pp) cc_final: 0.6634 (mp)
REVERT: A  723 LEU cc_start: 0.8934 (mt) cc_final: 0.8516 (tt)
REVERT: A  734 PHE cc_start: 0.8041 (t80) cc_final: 0.7386 (t80)
REVERT: A  737 ILE cc_start: 0.8541 (mm) cc_final: 0.8278 (tt)
REVERT: A  742 MET cc_start: 0.6521 (tpt) cc_final: 0.6214 (mtm)
REVERT: A  790 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6853 (tm-30)
REVERT: A  814 MET cc_start: 0.8369 (mmp) cc_final: 0.7998 (mmp)
REVERT: A  843 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6795 (tm-30)
REVERT: A  873 GLU cc_start: 0.8656 (mp0) cc_final: 0.8298 (mt-10)
REVERT: A  986 MET cc_start: 0.5254 (ppp) cc_final: 0.4989 (ppp)
REVERT: A 1047 LYS cc_start: 0.8183 (tmtt) cc_final: 0.7757 (tptt)
REVERT: A 1074 ASN cc_start: 0.7692 (m-40) cc_final: 0.7310 (t0)
REVERT: A 1077 VAL cc_start: 0.6230 (OUTLIER) cc_final: 0.5996 (m)
REVERT: A 1101 GLU cc_start: 0.9400 (mm-30) cc_final: 0.7949 (tp30)
REVERT: A 1112 GLU cc_start: 0.4983 (tm-30) cc_final: 0.4468 (tm-30)
REVERT: A 1150 TYR cc_start: 0.8091 (t80) cc_final: 0.7865 (t80)
  outliers start: 26
  outliers final: 14
  residues processed: 160
  average time/residue: 0.1799
  time to fit residues: 42.9747
Evaluate side-chains
  152 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  539 ARG
Chi-restraints excluded: chain A residue  613 PHE
Chi-restraints excluded: chain A residue  726 TRP
Chi-restraints excluded: chain A residue  790 GLN
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  908 GLU
Chi-restraints excluded: chain A residue 1051 ASN
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1100 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1244 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 93 optimal weight:    7.9990
   chunk 94 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 71 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.135788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.115054 restraints weight = 23605.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.118249 restraints weight = 13500.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.120451 restraints weight = 9324.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8820  Z= 0.149
  Angle     :  0.585   9.342  11911  Z= 0.303
  Chirality :  0.039   0.211   1367
  Planarity :  0.003   0.041   1517
  Dihedral  :  4.109  28.892   1195
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 19.31 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.52 (0.25), residues: 1104
  helix:  1.55 (0.20), residues: 678
  sheet: -0.62 (0.67), residues: 63
  loop : -1.87 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A1125 
 HIS   0.008   0.001   HIS A 375 
 PHE   0.016   0.001   PHE A 715 
 TYR   0.013   0.002   TYR A 870 
 ARG   0.004   0.000   ARG A1240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03908 (  554)
  hydrogen bonds       : angle       4.22127 ( 1632)
  covalent geometry    : bond        0.00330 ( 8820)
  covalent geometry    : angle       0.58521 (11911)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 145
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7879 (mp)
REVERT: A   64 PHE cc_start: 0.7798 (m-10) cc_final: 0.7357 (t80)
REVERT: A  133 MET cc_start: 0.8133 (ptt) cc_final: 0.7396 (ptt)
REVERT: A  142 TYR cc_start: 0.8740 (t80) cc_final: 0.8136 (t80)
REVERT: A  168 MET cc_start: 0.9044 (mmm) cc_final: 0.8542 (mmm)
REVERT: A  190 ASP cc_start: 0.9045 (m-30) cc_final: 0.8642 (m-30)
REVERT: A  267 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7453 (tp30)
REVERT: A  293 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8428 (mm)
REVERT: A  311 MET cc_start: 0.7739 (mtt) cc_final: 0.7342 (mtm)
REVERT: A  326 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7655 (m-80)
REVERT: A  334 MET cc_start: 0.4842 (mmt) cc_final: 0.4173 (ttm)
REVERT: A  355 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6527 (m-80)
REVERT: A  496 ILE cc_start: 0.6280 (OUTLIER) cc_final: 0.6057 (mp)
REVERT: A  734 PHE cc_start: 0.8154 (t80) cc_final: 0.7472 (t80)
REVERT: A  742 MET cc_start: 0.6422 (tpt) cc_final: 0.6161 (mtm)
REVERT: A  790 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6817 (tm-30)
REVERT: A  814 MET cc_start: 0.8378 (mmp) cc_final: 0.7900 (mmp)
REVERT: A  843 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6832 (tm-30)
REVERT: A  873 GLU cc_start: 0.8775 (mp0) cc_final: 0.8356 (mt-10)
REVERT: A  968 PHE cc_start: 0.8264 (m-80) cc_final: 0.7988 (m-80)
REVERT: A  986 MET cc_start: 0.5530 (OUTLIER) cc_final: 0.5065 (ppp)
REVERT: A  992 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.4347 (m-80)
REVERT: A 1020 MET cc_start: 0.8730 (tpt) cc_final: 0.8415 (tpt)
REVERT: A 1047 LYS cc_start: 0.8118 (tmtt) cc_final: 0.7777 (tptt)
REVERT: A 1074 ASN cc_start: 0.7502 (m-40) cc_final: 0.7246 (t0)
REVERT: A 1077 VAL cc_start: 0.6183 (OUTLIER) cc_final: 0.5896 (m)
REVERT: A 1101 GLU cc_start: 0.9315 (mm-30) cc_final: 0.7865 (tp30)
REVERT: A 1112 GLU cc_start: 0.4940 (tm-30) cc_final: 0.4447 (tm-30)
REVERT: A 1150 TYR cc_start: 0.8268 (t80) cc_final: 0.8024 (t80)
REVERT: A 1217 ASP cc_start: 0.5099 (p0) cc_final: 0.4876 (p0)
  outliers start: 42
  outliers final: 22
  residues processed: 169
  average time/residue: 0.1840
  time to fit residues: 46.4674
Evaluate side-chains
  164 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 132
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  613 PHE
Chi-restraints excluded: chain A residue  726 TRP
Chi-restraints excluded: chain A residue  790 GLN
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain A residue  813 MET
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  908 GLU
Chi-restraints excluded: chain A residue  926 SER
Chi-restraints excluded: chain A residue  986 MET
Chi-restraints excluded: chain A residue  992 TYR
Chi-restraints excluded: chain A residue 1051 ASN
Chi-restraints excluded: chain A residue 1067 VAL
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1100 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1244 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 53 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 ASN
** A1147 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 = 0.4094 r_free = 0.4094 target = 0.133048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.112056 restraints weight = 23636.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.115189 restraints weight = 13589.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.117334 restraints weight = 9436.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8820  Z= 0.198
  Angle     :  0.631   9.853  11911  Z= 0.330
  Chirality :  0.041   0.222   1367
  Planarity :  0.004   0.043   1517
  Dihedral  :  4.282  30.206   1195
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 21.47 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.42 (0.25), residues: 1104
  helix:  1.45 (0.20), residues: 677
  sheet: -0.58 (0.67), residues: 63
  loop : -1.86 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1125 
 HIS   0.008   0.001   HIS A 375 
 PHE   0.018   0.002   PHE A 715 
 TYR   0.014   0.002   TYR A 992 
 ARG   0.007   0.001   ARG A 539 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04139 (  554)
  hydrogen bonds       : angle       4.43886 ( 1632)
  covalent geometry    : bond        0.00435 ( 8820)
  covalent geometry    : angle       0.63071 (11911)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 130
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7962 (mp)
REVERT: A   64 PHE cc_start: 0.7824 (m-10) cc_final: 0.7318 (t80)
REVERT: A   80 MET cc_start: 0.6328 (ptt) cc_final: 0.6118 (ptt)
REVERT: A  142 TYR cc_start: 0.8807 (t80) cc_final: 0.8305 (t80)
REVERT: A  143 MET cc_start: 0.8081 (mtm) cc_final: 0.7756 (mtm)
REVERT: A  168 MET cc_start: 0.8947 (mmm) cc_final: 0.8344 (mmm)
REVERT: A  190 ASP cc_start: 0.9073 (m-30) cc_final: 0.8644 (m-30)
REVERT: A  267 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7460 (tp30)
REVERT: A  293 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8418 (mm)
REVERT: A  326 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7850 (m-80)
REVERT: A  334 MET cc_start: 0.4907 (mmt) cc_final: 0.4340 (ttt)
REVERT: A  355 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6671 (m-80)
REVERT: A  717 LYS cc_start: 0.8740 (pttp) cc_final: 0.8391 (ptmm)
REVERT: A  734 PHE cc_start: 0.8112 (t80) cc_final: 0.7575 (t80)
REVERT: A  742 MET cc_start: 0.6778 (tpt) cc_final: 0.6497 (mtm)
REVERT: A  790 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7264 (tm-30)
REVERT: A  814 MET cc_start: 0.8207 (mmp) cc_final: 0.7499 (mmp)
REVERT: A  843 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6701 (tm-30)
REVERT: A  873 GLU cc_start: 0.8769 (mp0) cc_final: 0.8380 (mt-10)
REVERT: A  968 PHE cc_start: 0.8386 (m-80) cc_final: 0.8064 (m-80)
REVERT: A  986 MET cc_start: 0.6211 (ppp) cc_final: 0.5561 (ppp)
REVERT: A  992 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.4444 (m-80)
REVERT: A 1047 LYS cc_start: 0.8239 (tmtt) cc_final: 0.7886 (tptt)
REVERT: A 1074 ASN cc_start: 0.7374 (m-40) cc_final: 0.7158 (t0)
REVERT: A 1077 VAL cc_start: 0.6213 (OUTLIER) cc_final: 0.5990 (m)
REVERT: A 1101 GLU cc_start: 0.9238 (mm-30) cc_final: 0.7927 (tp30)
REVERT: A 1150 TYR cc_start: 0.8345 (t80) cc_final: 0.7956 (t80)
REVERT: A 1217 ASP cc_start: 0.5501 (p0) cc_final: 0.5011 (p0)
REVERT: A 1223 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5683 (mp)
  outliers start: 43
  outliers final: 28
  residues processed: 160
  average time/residue: 0.1761
  time to fit residues: 41.3574
Evaluate side-chains
  158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 121
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  613 PHE
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  790 GLN
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain A residue  813 MET
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  908 GLU
Chi-restraints excluded: chain A residue  926 SER
Chi-restraints excluded: chain A residue  992 TYR
Chi-restraints excluded: chain A residue 1051 ASN
Chi-restraints excluded: chain A residue 1067 VAL
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1100 LEU
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1223 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1244 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 92 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 108 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 109 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 86 optimal weight:    0.1980
   chunk 52 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 144 GLN
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1147 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 = 0.4125 r_free = 0.4125 target = 0.135187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.114741 restraints weight = 23477.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.117972 restraints weight = 13438.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.120102 restraints weight = 9255.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8820  Z= 0.129
  Angle     :  0.614  12.291  11911  Z= 0.308
  Chirality :  0.039   0.167   1367
  Planarity :  0.003   0.045   1517
  Dihedral  :  4.081  26.746   1195
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 22.76 %
    Favored  : 73.25 %
  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:  0.59 (0.25), residues: 1104
  helix:  1.61 (0.20), residues: 677
  sheet: -0.63 (0.67), residues: 61
  loop : -1.82 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A1125 
 HIS   0.007   0.001   HIS A 375 
 PHE   0.014   0.001   PHE A 715 
 TYR   0.010   0.001   TYR A 322 
 ARG   0.003   0.000   ARG A1240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03738 (  554)
  hydrogen bonds       : angle       4.18210 ( 1632)
  covalent geometry    : bond        0.00294 ( 8820)
  covalent geometry    : angle       0.61354 (11911)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 138
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 PHE cc_start: 0.7728 (m-10) cc_final: 0.7342 (t80)
REVERT: A  142 TYR cc_start: 0.8752 (t80) cc_final: 0.8322 (t80)
REVERT: A  143 MET cc_start: 0.8182 (mtm) cc_final: 0.7842 (mtp)
REVERT: A  168 MET cc_start: 0.8918 (mmm) cc_final: 0.8354 (mmm)
REVERT: A  190 ASP cc_start: 0.9043 (m-30) cc_final: 0.8646 (m-30)
REVERT: A  267 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7524 (tp30)
REVERT: A  282 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6876 (mm-40)
REVERT: A  293 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8351 (mm)
REVERT: A  326 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7886 (m-80)
REVERT: A  334 MET cc_start: 0.4875 (mmt) cc_final: 0.4343 (ttt)
REVERT: A  355 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.6525 (m-80)
REVERT: A  487 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7782 (pm20)
REVERT: A  717 LYS cc_start: 0.8702 (pttp) cc_final: 0.8474 (ptmm)
REVERT: A  734 PHE cc_start: 0.8068 (t80) cc_final: 0.7476 (t80)
REVERT: A  790 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6934 (tm-30)
REVERT: A  792 PHE cc_start: 0.8127 (t80) cc_final: 0.7917 (t80)
REVERT: A  814 MET cc_start: 0.7961 (mmp) cc_final: 0.7198 (mmp)
REVERT: A  843 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6753 (tm-30)
REVERT: A  968 PHE cc_start: 0.8331 (m-80) cc_final: 0.8001 (m-80)
REVERT: A  986 MET cc_start: 0.5436 (ppp) cc_final: 0.5195 (ppp)
REVERT: A  992 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.4297 (m-80)
REVERT: A 1047 LYS cc_start: 0.8224 (tmtt) cc_final: 0.7935 (tptt)
REVERT: A 1074 ASN cc_start: 0.7387 (m-40) cc_final: 0.7125 (t0)
REVERT: A 1101 GLU cc_start: 0.7954 (mm-30) cc_final: 0.6504 (tp30)
REVERT: A 1150 TYR cc_start: 0.8256 (t80) cc_final: 0.7924 (t80)
REVERT: A 1217 ASP cc_start: 0.6031 (p0) cc_final: 0.5703 (p0)
REVERT: A 1223 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5750 (mp)
  outliers start: 37
  outliers final: 21
  residues processed: 164
  average time/residue: 0.1718
  time to fit residues: 41.1517
Evaluate side-chains
  157 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  613 PHE
Chi-restraints excluded: chain A residue  790 GLN
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain A residue  813 MET
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  908 GLU
Chi-restraints excluded: chain A residue  926 SER
Chi-restraints excluded: chain A residue  992 TYR
Chi-restraints excluded: chain A residue 1051 ASN
Chi-restraints excluded: chain A residue 1067 VAL
Chi-restraints excluded: chain A residue 1100 LEU
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1223 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1244 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 60 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 43 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 ASN
** A1147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.132455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.111680 restraints weight = 24001.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.114834 restraints weight = 13917.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.116940 restraints weight = 9715.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.3437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8820  Z= 0.178
  Angle     :  0.641  11.001  11911  Z= 0.328
  Chirality :  0.041   0.255   1367
  Planarity :  0.004   0.043   1517
  Dihedral  :  4.134  19.216   1193
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 22.55 %
    Favored  : 73.14 %
  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:  0.48 (0.25), residues: 1104
  helix:  1.47 (0.20), residues: 677
  sheet: -0.57 (0.69), residues: 61
  loop : -1.77 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A1125 
 HIS   0.008   0.001   HIS A 375 
 PHE   0.031   0.002   PHE A 532 
 TYR   0.015   0.002   TYR A 992 
 ARG   0.005   0.001   ARG A 539 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04039 (  554)
  hydrogen bonds       : angle       4.38536 ( 1632)
  covalent geometry    : bond        0.00399 ( 8820)
  covalent geometry    : angle       0.64126 (11911)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 124
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 PHE cc_start: 0.7784 (m-10) cc_final: 0.7340 (t80)
REVERT: A  142 TYR cc_start: 0.8776 (t80) cc_final: 0.8267 (t80)
REVERT: A  143 MET cc_start: 0.8323 (mtm) cc_final: 0.8085 (mtp)
REVERT: A  168 MET cc_start: 0.8949 (mmm) cc_final: 0.8342 (mmm)
REVERT: A  190 ASP cc_start: 0.9062 (m-30) cc_final: 0.8628 (m-30)
REVERT: A  267 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7546 (tp30)
REVERT: A  282 GLN cc_start: 0.7404 (mm-40) cc_final: 0.6984 (mm-40)
REVERT: A  293 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8407 (mm)
REVERT: A  326 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7870 (m-80)
REVERT: A  334 MET cc_start: 0.4549 (mmt) cc_final: 0.4017 (ttt)
REVERT: A  355 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6815 (m-80)
REVERT: A  435 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7724 (mm)
REVERT: A  487 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8104 (pm20)
REVERT: A  734 PHE cc_start: 0.8128 (t80) cc_final: 0.7572 (t80)
REVERT: A  790 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7279 (tm-30)
REVERT: A  814 MET cc_start: 0.8030 (mmp) cc_final: 0.7179 (mmp)
REVERT: A  843 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6493 (tm-30)
REVERT: A  968 PHE cc_start: 0.8373 (m-80) cc_final: 0.8069 (m-80)
REVERT: A  992 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.4406 (m-80)
REVERT: A 1047 LYS cc_start: 0.8298 (tmtt) cc_final: 0.7949 (tptt)
REVERT: A 1150 TYR cc_start: 0.8399 (t80) cc_final: 0.7947 (t80)
REVERT: A 1217 ASP cc_start: 0.4533 (p0) cc_final: 0.4027 (p0)
REVERT: A 1223 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5801 (mp)
  outliers start: 40
  outliers final: 24
  residues processed: 152
  average time/residue: 0.1638
  time to fit residues: 37.1374
Evaluate side-chains
  152 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 119
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  613 PHE
Chi-restraints excluded: chain A residue  790 GLN
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain A residue  813 MET
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  992 TYR
Chi-restraints excluded: chain A residue 1051 ASN
Chi-restraints excluded: chain A residue 1067 VAL
Chi-restraints excluded: chain A residue 1100 LEU
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1223 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1244 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 51 optimal weight:    0.3980
   chunk 65 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 106 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.134535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.114017 restraints weight = 23664.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.117291 restraints weight = 13482.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.119456 restraints weight = 9259.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8820  Z= 0.130
  Angle     :  0.638   9.168  11911  Z= 0.319
  Chirality :  0.040   0.212   1367
  Planarity :  0.003   0.043   1517
  Dihedral  :  4.025  18.565   1193
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 24.38 %
    Favored  : 72.17 %
  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:  0.56 (0.25), residues: 1104
  helix:  1.43 (0.19), residues: 697
  sheet: -0.45 (0.70), residues: 60
  loop : -1.69 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A1125 
 HIS   0.007   0.001   HIS A 375 
 PHE   0.028   0.001   PHE A 532 
 TYR   0.015   0.001   TYR A1284 
 ARG   0.003   0.000   ARG A 539 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (  554)
  hydrogen bonds       : angle       4.17749 ( 1632)
  covalent geometry    : bond        0.00291 ( 8820)
  covalent geometry    : angle       0.63763 (11911)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 PHE cc_start: 0.7725 (m-10) cc_final: 0.7362 (t80)
REVERT: A  142 TYR cc_start: 0.8759 (t80) cc_final: 0.8253 (t80)
REVERT: A  143 MET cc_start: 0.8247 (mtm) cc_final: 0.7979 (mtp)
REVERT: A  168 MET cc_start: 0.8948 (mmm) cc_final: 0.8367 (mmm)
REVERT: A  190 ASP cc_start: 0.9051 (m-30) cc_final: 0.8656 (m-30)
REVERT: A  267 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7487 (tp30)
REVERT: A  282 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7362 (mm-40)
REVERT: A  293 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8347 (mm)
REVERT: A  311 MET cc_start: 0.8089 (mtt) cc_final: 0.7607 (mtm)
REVERT: A  326 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7870 (m-80)
REVERT: A  334 MET cc_start: 0.4542 (mmt) cc_final: 0.4014 (ttt)
REVERT: A  355 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.6724 (m-80)
REVERT: A  487 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8025 (pm20)
REVERT: A  734 PHE cc_start: 0.8091 (t80) cc_final: 0.7535 (t80)
REVERT: A  790 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6937 (tm-30)
REVERT: A  814 MET cc_start: 0.7902 (mmp) cc_final: 0.7100 (mmp)
REVERT: A  843 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6601 (tm-30)
REVERT: A  968 PHE cc_start: 0.8328 (m-80) cc_final: 0.8015 (m-80)
REVERT: A 1020 MET cc_start: 0.8835 (tpt) cc_final: 0.8553 (tpt)
REVERT: A 1047 LYS cc_start: 0.8304 (tmtt) cc_final: 0.8007 (tptt)
REVERT: A 1150 TYR cc_start: 0.8283 (t80) cc_final: 0.7827 (t80)
REVERT: A 1217 ASP cc_start: 0.5846 (p0) cc_final: 0.5522 (p0)
  outliers start: 32
  outliers final: 25
  residues processed: 151
  average time/residue: 0.1855
  time to fit residues: 42.4137
Evaluate side-chains
  153 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  613 PHE
Chi-restraints excluded: chain A residue  790 GLN
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain A residue  813 MET
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue 1051 ASN
Chi-restraints excluded: chain A residue 1067 VAL
Chi-restraints excluded: chain A residue 1100 LEU
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1223 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1244 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 110 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 107 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 70 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 101 optimal weight:    6.9990
   chunk 94 optimal weight:    0.0000
   chunk 22 optimal weight:    7.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 ASN
** A1147 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 = 0.133500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.112869 restraints weight = 23725.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.116145 restraints weight = 13596.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.118262 restraints weight = 9376.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8820  Z= 0.153
  Angle     :  0.645   9.469  11911  Z= 0.324
  Chirality :  0.041   0.281   1367
  Planarity :  0.004   0.044   1517
  Dihedral  :  4.073  18.969   1193
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 25.03 %
    Favored  : 71.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.25), residues: 1104
  helix:  1.41 (0.19), residues: 692
  sheet: -0.48 (0.70), residues: 61
  loop : -1.75 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A1125 
 HIS   0.007   0.001   HIS A 375 
 PHE   0.025   0.001   PHE A 532 
 TYR   0.013   0.002   TYR A1284 
 ARG   0.005   0.000   ARG A 539 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03908 (  554)
  hydrogen bonds       : angle       4.29352 ( 1632)
  covalent geometry    : bond        0.00344 ( 8820)
  covalent geometry    : angle       0.64532 (11911)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 122
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 PHE cc_start: 0.7761 (m-10) cc_final: 0.7387 (t80)
REVERT: A  130 TYR cc_start: 0.6197 (m-10) cc_final: 0.5519 (m-10)
REVERT: A  142 TYR cc_start: 0.8754 (t80) cc_final: 0.8236 (t80)
REVERT: A  168 MET cc_start: 0.8970 (mmm) cc_final: 0.8378 (mmm)
REVERT: A  190 ASP cc_start: 0.9059 (m-30) cc_final: 0.8648 (m-30)
REVERT: A  267 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7552 (tp30)
REVERT: A  282 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7047 (mm-40)
REVERT: A  293 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8382 (mm)
REVERT: A  311 MET cc_start: 0.8105 (mtt) cc_final: 0.7611 (mtm)
REVERT: A  326 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7547 (m-80)
REVERT: A  334 MET cc_start: 0.4572 (mmt) cc_final: 0.4029 (ttt)
REVERT: A  355 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6784 (m-10)
REVERT: A  365 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8048 (mt0)
REVERT: A  487 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8147 (pm20)
REVERT: A  734 PHE cc_start: 0.8138 (t80) cc_final: 0.7575 (t80)
REVERT: A  790 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7267 (tm-30)
REVERT: A  814 MET cc_start: 0.7961 (mmp) cc_final: 0.7090 (mmp)
REVERT: A  843 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6441 (tm-30)
REVERT: A  968 PHE cc_start: 0.8352 (m-80) cc_final: 0.8045 (m-80)
REVERT: A 1020 MET cc_start: 0.8683 (tpt) cc_final: 0.8390 (tpt)
REVERT: A 1047 LYS cc_start: 0.8333 (tmtt) cc_final: 0.8051 (tptt)
REVERT: A 1150 TYR cc_start: 0.8369 (t80) cc_final: 0.7896 (t80)
REVERT: A 1217 ASP cc_start: 0.5840 (p0) cc_final: 0.5529 (p0)
REVERT: A 1223 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5851 (mp)
  outliers start: 34
  outliers final: 26
  residues processed: 145
  average time/residue: 0.1832
  time to fit residues: 40.1106
Evaluate side-chains
  151 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 118
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  613 PHE
Chi-restraints excluded: chain A residue  790 GLN
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain A residue  813 MET
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  933 PHE
Chi-restraints excluded: chain A residue 1051 ASN
Chi-restraints excluded: chain A residue 1067 VAL
Chi-restraints excluded: chain A residue 1100 LEU
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1223 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1244 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 101 optimal weight:   10.0000
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 826 ASN
** A1147 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 = 0.4111 r_free = 0.4111 target = 0.134407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.113622 restraints weight = 23770.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.116917 restraints weight = 13529.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.119104 restraints weight = 9310.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.3822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8820  Z= 0.137
  Angle     :  0.659   9.713  11911  Z= 0.327
  Chirality :  0.041   0.260   1367
  Planarity :  0.003   0.045   1517
  Dihedral  :  4.053  19.869   1193
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 25.89 %
    Favored  : 70.66 %
  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:  0.59 (0.25), residues: 1104
  helix:  1.45 (0.19), residues: 692
  sheet:  0.69 (0.84), residues: 43
  loop : -1.74 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A1125 
 HIS   0.007   0.001   HIS A 375 
 PHE   0.023   0.001   PHE A 532 
 TYR   0.019   0.002   TYR A1061 
 ARG   0.003   0.000   ARG A 539 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03762 (  554)
  hydrogen bonds       : angle       4.21907 ( 1632)
  covalent geometry    : bond        0.00310 ( 8820)
  covalent geometry    : angle       0.65852 (11911)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 120
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 PHE cc_start: 0.7712 (m-10) cc_final: 0.7372 (t80)
REVERT: A   80 MET cc_start: 0.5776 (ptt) cc_final: 0.5218 (tpt)
REVERT: A  130 TYR cc_start: 0.6192 (m-10) cc_final: 0.5883 (m-10)
REVERT: A  142 TYR cc_start: 0.8755 (t80) cc_final: 0.8204 (t80)
REVERT: A  168 MET cc_start: 0.8981 (mmm) cc_final: 0.8398 (mmm)
REVERT: A  190 ASP cc_start: 0.9044 (m-30) cc_final: 0.8647 (m-30)
REVERT: A  267 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7467 (tp30)
REVERT: A  282 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7488 (mm-40)
REVERT: A  293 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8366 (mm)
REVERT: A  311 MET cc_start: 0.8087 (mtt) cc_final: 0.7575 (mtm)
REVERT: A  326 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7540 (m-80)
REVERT: A  334 MET cc_start: 0.4551 (mmt) cc_final: 0.4027 (ttt)
REVERT: A  355 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6662 (m-10)
REVERT: A  365 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8049 (mt0)
REVERT: A  487 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8210 (pm20)
REVERT: A  734 PHE cc_start: 0.8134 (t80) cc_final: 0.7584 (t80)
REVERT: A  790 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7234 (tm-30)
REVERT: A  814 MET cc_start: 0.7902 (mmp) cc_final: 0.7055 (mmp)
REVERT: A  843 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6580 (tm-30)
REVERT: A  968 PHE cc_start: 0.8337 (m-80) cc_final: 0.7990 (m-80)
REVERT: A 1020 MET cc_start: 0.8657 (tpt) cc_final: 0.8346 (tpt)
REVERT: A 1047 LYS cc_start: 0.8348 (tmtt) cc_final: 0.8066 (tptt)
REVERT: A 1150 TYR cc_start: 0.8314 (t80) cc_final: 0.7802 (t80)
REVERT: A 1217 ASP cc_start: 0.5784 (p0) cc_final: 0.5477 (p0)
  outliers start: 32
  outliers final: 25
  residues processed: 141
  average time/residue: 0.1708
  time to fit residues: 35.7909
Evaluate side-chains
  150 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  326 PHE
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  487 GLN
Chi-restraints excluded: chain A residue  507 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  613 PHE
Chi-restraints excluded: chain A residue  790 GLN
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain A residue  813 MET
Chi-restraints excluded: chain A residue  843 GLN
Chi-restraints excluded: chain A residue  933 PHE
Chi-restraints excluded: chain A residue 1051 ASN
Chi-restraints excluded: chain A residue 1067 VAL
Chi-restraints excluded: chain A residue 1100 LEU
Chi-restraints excluded: chain A residue 1132 ILE
Chi-restraints excluded: chain A residue 1223 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1244 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 102 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 94 optimal weight:    0.0670
   chunk 65 optimal weight:    0.6980
   overall best weight:    1.3122

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 ASN
** A1147 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 = 0.4096 r_free = 0.4096 target = 0.133488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.112857 restraints weight = 23853.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.116114 restraints weight = 13593.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.118250 restraints weight = 9345.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.3936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8820  Z= 0.153
  Angle     :  0.651   9.713  11911  Z= 0.327
  Chirality :  0.041   0.243   1367
  Planarity :  0.004   0.045   1517
  Dihedral  :  4.074  20.460   1193
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 25.24 %
    Favored  : 70.87 %
  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:  0.55 (0.25), residues: 1104
  helix:  1.41 (0.19), residues: 690
  sheet:  0.06 (0.79), residues: 50
  loop : -1.67 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A1125 
 HIS   0.007   0.001   HIS A 375 
 PHE   0.023   0.001   PHE A 532 
 TYR   0.018   0.002   TYR A1061 
 ARG   0.003   0.000   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03913 (  554)
  hydrogen bonds       : angle       4.29563 ( 1632)
  covalent geometry    : bond        0.00343 ( 8820)
  covalent geometry    : angle       0.65127 (11911)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2770.71 seconds
wall clock time: 49 minutes 10.96 seconds (2950.96 seconds total)