Starting phenix.real_space_refine
on Fri Feb 14 11:50:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sfj_40443/02_2025/8sfj_40443.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sfj_40443/02_2025/8sfj_40443.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sfj_40443/02_2025/8sfj_40443.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sfj_40443/02_2025/8sfj_40443.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sfj_40443/02_2025/8sfj_40443.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sfj_40443/02_2025/8sfj_40443.cif"
  }
  resolution = 3.6
  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=  -0.001 sd=   0.029
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: 5
    Type Number    sf(0)   Gaussians
     P      96      5.49       5
     S      20      5.16       5
     C    6225      2.51       5
     N    1740      2.21       5
     O    2126      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10207
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1001, 8202
          Classifications: {'peptide': 1001}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 41, 'TRANS': 959}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 611
          Classifications: {'RNA': 29}
          Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 6, 'rna3p': 22}
    Chain: "C"
      Number of atoms: 696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 696
          Classifications: {'DNA': 34}
          Link IDs: {'rna3p': 33}
    Chain: "D"
      Number of atoms: 698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 698
          Classifications: {'DNA': 34}
          Link IDs: {'rna3p': 33}
  Time building chain proxies: 7.06, per 1000 atoms: 0.69
  Number of scatterers: 10207
  At special positions: 0
  Unit cell: (83.3, 98.294, 149.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P      96     15.00
     O    2126      8.00
     N    1740      7.00
     C    6225      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: 2.57
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1900

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 9 sheets defined
      49.8% alpha, 13.5% beta
      34 base pairs and 65 stacking pairs defined.
    Time for finding SS restraints: 3.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 7
      removed outlier: 3.578A  pdb=" N   PHE A   7 " --> pdb=" O   PHE A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 35
    Processing helix  chain 'A' and resid 35 through 67
      removed outlier: 3.727A  pdb=" N   GLU A  39 " --> pdb=" O   GLY A  35 " (cutoff:3.500A)
      Proline residue:  A  52  - end of helix
    Processing helix  chain 'A' and resid 73 through 87
    Processing helix  chain 'A' and resid 88 through 111
    Processing helix  chain 'A' and resid 118 through 132
    Processing helix  chain 'A' and resid 133 through 138
      removed outlier: 7.052A  pdb=" N   GLU A 136 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU A 137 " --> pdb=" O   LYS A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 146
      removed outlier: 3.914A  pdb=" N   LYS A 144 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 161
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 169 through 181
    Processing helix  chain 'A' and resid 188 through 195
    Processing helix  chain 'A' and resid 196 through 215
      removed outlier: 4.311A  pdb=" N   LYS A 200 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 230
      removed outlier: 4.243A  pdb=" N   GLU A 220 " --> pdb=" O   PRO A 216 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   HIS A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 241
    Processing helix  chain 'A' and resid 242 through 248
    Processing helix  chain 'A' and resid 251 through 264
      removed outlier: 3.635A  pdb=" N   LEU A 262 " --> pdb=" O   TYR A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 287
    Processing helix  chain 'A' and resid 289 through 297
    Processing helix  chain 'A' and resid 548 through 553
    Processing helix  chain 'A' and resid 600 through 605
    Processing helix  chain 'A' and resid 612 through 622
    Processing helix  chain 'A' and resid 639 through 647
      removed outlier: 3.776A  pdb=" N   TYR A 643 " --> pdb=" O   THR A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 664
      removed outlier: 3.751A  pdb=" N   ALA A 660 " --> pdb=" O   GLN A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 687
    Processing helix  chain 'A' and resid 700 through 704
      removed outlier: 3.599A  pdb=" N   TYR A 704 " --> pdb=" O   SER A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 715
      removed outlier: 3.615A  pdb=" N   TYR A 710 " --> pdb=" O   ASP A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 737
    Processing helix  chain 'A' and resid 759 through 769
      removed outlier: 3.696A  pdb=" N   PHE A 769 " --> pdb=" O   TRP A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 776
    Processing helix  chain 'A' and resid 887 through 899
    Processing helix  chain 'A' and resid 940 through 949
      removed outlier: 4.044A  pdb=" N   ASN A 946 " --> pdb=" O   LYS A 942 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LYS A 949 " --> pdb=" O   ASP A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 987
      removed outlier: 4.055A  pdb=" N   HIS A 977 " --> pdb=" O   SER A 973 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLU A 978 " --> pdb=" O   GLN A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 995 through 998
    Processing helix  chain 'A' and resid 1008 through 1025
      removed outlier: 3.809A  pdb=" N   TYR A1012 " --> pdb=" O   GLU A1008 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   CYS A1025 " --> pdb=" O   ASP A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1090 through 1100
    Processing helix  chain 'A' and resid 1177 through 1187
    Processing helix  chain 'A' and resid 1198 through 1206
      removed outlier: 4.360A  pdb=" N   LYS A1202 " --> pdb=" O   ASN A1198 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   ASN A1206 " --> pdb=" O   LYS A1202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1208 through 1224
    Processing helix  chain 'A' and resid 1252 through 1254
      No H-bonds generated for 'chain 'A' and resid 1252 through 1254'
    Processing helix  chain 'A' and resid 1261 through 1284
    Processing helix  chain 'A' and resid 1294 through 1307
    Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 533
      removed outlier: 4.660A  pdb=" N   LEU A 787 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   PHE A 869 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   TYR A 563 " --> pdb=" O   ILE A 745 " (cutoff:3.500A)
      removed outlier: 11.319A  pdb=" N   ALA A 554 " --> pdb=" O   TYR A 595 " (cutoff:3.500A)
      removed outlier: 8.614A  pdb=" N   TYR A 595 " --> pdb=" O   ALA A 554 " (cutoff:3.500A)
      removed outlier: 5.482A  pdb=" N   LEU A 556 " --> pdb=" O   MET A 593 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533
      removed outlier: 4.660A  pdb=" N   LEU A 787 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 626 through 628
    Processing sheet with id=AA4, first strand: chain 'A' and resid 926 through 931
      removed outlier: 6.435A  pdb=" N   VAL A 919 " --> pdb=" O   LEU A 927 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   GLN A 929 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ILE A 917 " --> pdb=" O   GLN A 929 " (cutoff:3.500A)
      removed outlier: 4.986A  pdb=" N   SER A 931 " --> pdb=" O   ILE A 915 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ILE A 915 " --> pdb=" O   SER A 931 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ILE A 905 " --> pdb=" O   VAL A 991 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   GLU A 993 " --> pdb=" O   ILE A 905 " (cutoff:3.500A)
      removed outlier: 8.981A  pdb=" N   ILE A 907 " --> pdb=" O   GLU A 993 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   VAL A 990 " --> pdb=" O   PHE A1063 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   VAL A1065 " --> pdb=" O   VAL A 990 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   LEU A 992 " --> pdb=" O   VAL A1065 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1103 through 1106
      removed outlier: 4.037A  pdb=" N   PHE A1103 " --> pdb=" O   HIS A1116 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1145 through 1147
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1159 through 1161
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1164 through 1165
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1226 through 1229
      removed outlier: 4.241A  pdb=" N   PHE A1249 " --> pdb=" O   SER A1239 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1122 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      83 hydrogen bonds
      162 hydrogen bond angles
      0 basepair planarities
      34 basepair parallelities
      65 stacking parallelities
  Total time for adding SS restraints: 5.26

  Time building geometry restraints manager: 3.03 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2262
        1.33 -     1.46: 2968
        1.46 -     1.58: 5185
        1.58 -     1.70: 191
        1.70 -     1.82: 34
  Bond restraints: 10640
  Sorted by residual:
  bond pdb=" CB  ASN A1291 "
       pdb=" CG  ASN A1291 "
    ideal  model  delta    sigma   weight residual
    1.516  1.576 -0.060 2.50e-02 1.60e+03 5.71e+00
  bond pdb=" CA  ASN A1291 "
       pdb=" CB  ASN A1291 "
    ideal  model  delta    sigma   weight residual
    1.530  1.563 -0.034 1.50e-02 4.44e+03 4.99e+00
  bond pdb=" CB  ARG A1194 "
       pdb=" CG  ARG A1194 "
    ideal  model  delta    sigma   weight residual
    1.520  1.584 -0.064 3.00e-02 1.11e+03 4.55e+00
  bond pdb=" C1'  DT D  16 "
       pdb=" N1   DT D  16 "
    ideal  model  delta    sigma   weight residual
    1.490  1.552 -0.062 3.00e-02 1.11e+03 4.28e+00
  bond pdb=" CA  GLN A 987 "
       pdb=" CB  GLN A 987 "
    ideal  model  delta    sigma   weight residual
    1.530  1.560 -0.030 1.50e-02 4.44e+03 4.08e+00
  ... (remaining 10635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.82: 14565
        3.82 -     7.64: 167
        7.64 -    11.46: 62
       11.46 -    15.28: 9
       15.28 -    19.10: 3
  Bond angle restraints: 14806
  Sorted by residual:
  angle pdb=" CA  PRO A1256 "
        pdb=" N   PRO A1256 "
        pdb=" CD  PRO A1256 "
      ideal   model   delta    sigma   weight residual
     112.00  101.40   10.60 1.40e+00 5.10e-01 5.74e+01
  angle pdb=" O3'  DG D  17 "
        pdb=" P    DA D  18 "
        pdb=" OP1  DA D  18 "
      ideal   model   delta    sigma   weight residual
     108.00  127.10  -19.10 3.00e+00 1.11e-01 4.05e+01
  angle pdb=" CA  GLN A 987 "
        pdb=" CB  GLN A 987 "
        pdb=" CG  GLN A 987 "
      ideal   model   delta    sigma   weight residual
     114.10  126.82  -12.72 2.00e+00 2.50e-01 4.05e+01
  angle pdb=" CB  MET A 604 "
        pdb=" CG  MET A 604 "
        pdb=" SD  MET A 604 "
      ideal   model   delta    sigma   weight residual
     112.70  130.23  -17.53 3.00e+00 1.11e-01 3.41e+01
  angle pdb=" CA  ASN A1291 "
        pdb=" CB  ASN A1291 "
        pdb=" CG  ASN A1291 "
      ideal   model   delta    sigma   weight residual
     112.60  118.39   -5.79 1.00e+00 1.00e+00 3.35e+01
  ... (remaining 14801 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.11: 5554
       31.11 -    62.21: 624
       62.21 -    93.32: 52
       93.32 -   124.42: 1
      124.42 -   155.53: 3
  Dihedral angle restraints: 6234
    sinusoidal: 3291
      harmonic: 2943
  Sorted by residual:
  dihedral pdb=" O4'   C B  11 "
           pdb=" C1'   C B  11 "
           pdb=" N1    C B  11 "
           pdb=" C2    C B  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   44.47  155.53     1      1.50e+01 4.44e-03 8.15e+01
  dihedral pdb=" O4'   U B  12 "
           pdb=" C1'   U B  12 "
           pdb=" N1    U B  12 "
           pdb=" C2    U B  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   56.96  143.04     1      1.50e+01 4.44e-03 7.68e+01
  dihedral pdb=" CA  PRO A 700 "
           pdb=" C   PRO A 700 "
           pdb=" N   SER A 701 "
           pdb=" CA  SER A 701 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.31  -19.69     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 6231 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 1551
       0.120 -    0.240: 74
       0.240 -    0.360: 2
       0.360 -    0.480: 13
       0.480 -    0.600: 1
  Chirality restraints: 1641
  Sorted by residual:
  chirality pdb=" P    DA D  18 "
            pdb=" OP1  DA D  18 "
            pdb=" OP2  DA D  18 "
            pdb=" O5'  DA D  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.95   -0.60 2.00e-01 2.50e+01 9.01e+00
  chirality pdb=" P    DA D  14 "
            pdb=" OP1  DA D  14 "
            pdb=" OP2  DA D  14 "
            pdb=" O5'  DA D  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.81   -0.46 2.00e-01 2.50e+01 5.35e+00
  chirality pdb=" P    DA C  28 "
            pdb=" OP1  DA C  28 "
            pdb=" OP2  DA C  28 "
            pdb=" O5'  DA C  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.81   -0.46 2.00e-01 2.50e+01 5.31e+00
  ... (remaining 1638 not shown)

  Planarity restraints: 1559
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A1255 "    0.115 5.00e-02 4.00e+02   1.67e-01 4.48e+01
        pdb=" N   PRO A1256 "   -0.289 5.00e-02 4.00e+02
        pdb=" CA  PRO A1256 "    0.090 5.00e-02 4.00e+02
        pdb=" CD  PRO A1256 "    0.084 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1065 "   -0.097 5.00e-02 4.00e+02   1.44e-01 3.33e+01
        pdb=" N   PRO A1066 "    0.250 5.00e-02 4.00e+02
        pdb=" CA  PRO A1066 "   -0.078 5.00e-02 4.00e+02
        pdb=" CD  PRO A1066 "   -0.074 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1085 "    0.028 2.00e-02 2.50e+03   2.76e-02 1.91e+01
        pdb=" CG  TRP A1085 "   -0.071 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1085 "    0.040 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1085 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1085 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1085 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1085 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1085 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1085 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1085 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1556 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 608
        2.73 -     3.27: 9840
        3.27 -     3.81: 18235
        3.81 -     4.36: 21820
        4.36 -     4.90: 34103
  Nonbonded interactions: 84606
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 931 "
            pdb=" OD1 ASN A 933 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OG1 THR A 610 "
            pdb=" OE1 GLN A 611 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OG1 THR A   8 "
            pdb=" O   PRO A1042 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   THR A 167 "
            pdb=" OG  SER A 170 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" NZ  LYS A  59 "
            pdb=" OD1 ASP A 312 "
     model   vdw
     2.295 3.120
  ... (remaining 84601 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.920
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     30.810
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
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      :  0.005   0.067  10640  Z= 0.324
  Angle     :  1.186  19.101  14806  Z= 0.587
  Chirality :  0.068   0.600   1641
  Planarity :  0.009   0.167   1559
  Dihedral  : 22.090 155.528   4334
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  : 24.97 %
    Favored  : 74.80 %
  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: -0.53 (0.26), residues: 991
  helix: -0.35 (0.23), residues: 444
  sheet: -0.39 (0.41), residues: 140
  loop : -0.08 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.071   0.004   TRP A1085 
 HIS   0.034   0.002   HIS A1096 
 PHE   0.047   0.003   PHE A 619 
 TYR   0.050   0.003   TYR A1236 
 ARG   0.007   0.001   ARG A1003 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1055 MET cc_start: 0.7436 (ppp) cc_final: 0.6393 (ppp)
  outliers start: 2
  outliers final: 1
  residues processed: 61
  average time/residue: 0.2265
  time to fit residues: 20.4146
Evaluate side-chains
  45 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1080 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    7.9990
   chunk 81 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 84 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   chunk 63 optimal weight:    9.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 300 HIS
A 547 ASN
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 620 GLN
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 883 ASN
A 936 GLN
** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.042185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.029077 restraints weight = 76803.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.030075 restraints weight = 40827.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.030701 restraints weight = 28049.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.047  10640  Z= 0.468
  Angle     :  0.753  10.062  14806  Z= 0.409
  Chirality :  0.044   0.141   1641
  Planarity :  0.006   0.081   1559
  Dihedral  : 23.297 156.028   2280
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.60 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.27), residues: 991
  helix:  0.54 (0.24), residues: 448
  sheet: -0.41 (0.41), residues: 144
  loop :  0.33 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A1085 
 HIS   0.015   0.002   HIS A1096 
 PHE   0.022   0.002   PHE A1052 
 TYR   0.020   0.002   TYR A1173 
 ARG   0.005   0.001   ARG A 160 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 40
  time to evaluate  : 1.796 
Fit side-chains
   revert: symmetry clash
REVERT: A  782 ASN cc_start: 0.9308 (m-40) cc_final: 0.8801 (t0)
REVERT: A  786 GLU cc_start: 0.8084 (mp0) cc_final: 0.7798 (mp0)
REVERT: A 1018 MET cc_start: 0.8981 (mtm) cc_final: 0.8760 (mtm)
REVERT: A 1133 MET cc_start: 0.9228 (pmm) cc_final: 0.8826 (pmm)
REVERT: A 1280 HIS cc_start: 0.9252 (OUTLIER) cc_final: 0.8641 (t-90)
  outliers start: 34
  outliers final: 20
  residues processed: 69
  average time/residue: 0.2028
  time to fit residues: 21.5124
Evaluate side-chains
  60 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 39
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  575 TYR
Chi-restraints excluded: chain A residue  755 HIS
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1090 ASN
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1225 MET
Chi-restraints excluded: chain A residue 1247 VAL
Chi-restraints excluded: chain A residue 1280 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 84 optimal weight:    6.9990
   chunk 25 optimal weight:    0.5980
   chunk 47 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 85 optimal weight:    7.9990
   overall best weight:    3.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  30 HIS
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1143 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 = 0.3167 r_free = 0.3167 target = 0.041974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.028809 restraints weight = 75930.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.029821 restraints weight = 39986.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.030467 restraints weight = 27458.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  10640  Z= 0.312
  Angle     :  0.644   9.428  14806  Z= 0.351
  Chirality :  0.041   0.176   1641
  Planarity :  0.005   0.062   1559
  Dihedral  : 23.372 157.800   2280
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 19.82 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.28), residues: 991
  helix:  0.84 (0.24), residues: 451
  sheet: -0.45 (0.41), residues: 150
  loop :  0.45 (0.35), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1085 
 HIS   0.010   0.001   HIS A1096 
 PHE   0.011   0.001   PHE A 999 
 TYR   0.018   0.002   TYR A 764 
 ARG   0.004   0.000   ARG A1121 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 39
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
REVERT: A  782 ASN cc_start: 0.9295 (m-40) cc_final: 0.8729 (t0)
REVERT: A  786 GLU cc_start: 0.8081 (mp0) cc_final: 0.7724 (mp0)
REVERT: A  997 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7934 (m-80)
REVERT: A 1133 MET cc_start: 0.9197 (pmm) cc_final: 0.8898 (pmm)
REVERT: A 1280 HIS cc_start: 0.9301 (OUTLIER) cc_final: 0.8729 (t-90)
  outliers start: 41
  outliers final: 24
  residues processed: 76
  average time/residue: 0.2099
  time to fit residues: 25.0835
Evaluate side-chains
  63 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 37
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  536 GLN
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  624 THR
Chi-restraints excluded: chain A residue  755 HIS
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue  997 PHE
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1247 VAL
Chi-restraints excluded: chain A residue 1280 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 96 optimal weight:    7.9990
   chunk 9 optimal weight:    9.9990
   chunk 84 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 178 ASN
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN
** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1279 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.042135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.029083 restraints weight = 75781.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.030079 restraints weight = 39907.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.030702 restraints weight = 27580.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  10640  Z= 0.314
  Angle     :  0.628   8.991  14806  Z= 0.343
  Chirality :  0.041   0.173   1641
  Planarity :  0.004   0.058   1559
  Dihedral  : 23.388 157.659   2280
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 21.84 %
    Favored  : 74.02 %
  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:  0.70 (0.28), residues: 991
  helix:  0.99 (0.24), residues: 451
  sheet: -0.48 (0.41), residues: 149
  loop :  0.46 (0.36), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1085 
 HIS   0.008   0.001   HIS A1096 
 PHE   0.013   0.001   PHE A1249 
 TYR   0.016   0.002   TYR A  61 
 ARG   0.003   0.000   ARG A1121 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 38
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  782 ASN cc_start: 0.9294 (m-40) cc_final: 0.8699 (t0)
REVERT: A  786 GLU cc_start: 0.8099 (mp0) cc_final: 0.7717 (mp0)
REVERT: A  938 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8632 (t80)
REVERT: A 1018 MET cc_start: 0.9040 (mtm) cc_final: 0.8830 (mtm)
REVERT: A 1133 MET cc_start: 0.9177 (pmm) cc_final: 0.8948 (pmm)
REVERT: A 1280 HIS cc_start: 0.9293 (OUTLIER) cc_final: 0.8676 (t-90)
  outliers start: 37
  outliers final: 23
  residues processed: 72
  average time/residue: 0.2022
  time to fit residues: 22.5669
Evaluate side-chains
  62 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 37
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain A residue  624 THR
Chi-restraints excluded: chain A residue  688 THR
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  755 HIS
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  938 PHE
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1280 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 100 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 85 optimal weight:   20.0000
   chunk 39 optimal weight:    7.9990
   chunk 40 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN
** A1143 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 = 0.3130 r_free = 0.3130 target = 0.040306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.027287 restraints weight = 78624.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.028280 restraints weight = 41289.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.028879 restraints weight = 28415.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048  10640  Z= 0.433
  Angle     :  0.696   8.291  14806  Z= 0.382
  Chirality :  0.043   0.158   1641
  Planarity :  0.005   0.054   1559
  Dihedral  : 23.731 159.460   2280
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 22.84 %
    Favored  : 71.67 %
  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:  0.37 (0.27), residues: 991
  helix:  0.68 (0.24), residues: 449
  sheet: -0.52 (0.42), residues: 131
  loop :  0.25 (0.34), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A1085 
 HIS   0.009   0.002   HIS A 618 
 PHE   0.016   0.002   PHE A1052 
 TYR   0.020   0.002   TYR A  61 
 ARG   0.005   0.001   ARG A 912 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 34
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7940 (ttpp)
REVERT: A  593 MET cc_start: 0.9503 (ppp) cc_final: 0.9225 (ppp)
REVERT: A  938 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8669 (t80)
REVERT: A 1199 ILE cc_start: 0.9602 (OUTLIER) cc_final: 0.9384 (mm)
REVERT: A 1280 HIS cc_start: 0.9266 (OUTLIER) cc_final: 0.8652 (t-90)
  outliers start: 49
  outliers final: 30
  residues processed: 80
  average time/residue: 0.2050
  time to fit residues: 25.2550
Evaluate side-chains
  67 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 33
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain A residue  624 THR
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  755 HIS
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  938 PHE
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1199 ILE
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1247 VAL
Chi-restraints excluded: chain A residue 1277 LEU
Chi-restraints excluded: chain A residue 1280 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:   20.0000
   chunk 14 optimal weight:    9.9990
   chunk 59 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 107 optimal weight:   30.0000
   chunk 68 optimal weight:    0.8980
   chunk 80 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 GLN
A 647 ASN
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1091 HIS
A1122 ASN
** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.042037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.028977 restraints weight = 74921.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.030033 restraints weight = 38831.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.030695 restraints weight = 26290.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10640  Z= 0.179
  Angle     :  0.612   8.682  14806  Z= 0.327
  Chirality :  0.040   0.225   1641
  Planarity :  0.004   0.056   1559
  Dihedral  : 23.442 156.941   2280
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 24.97 %
    Favored  : 71.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.28), residues: 991
  helix:  1.13 (0.25), residues: 449
  sheet: -0.51 (0.40), residues: 148
  loop :  0.47 (0.35), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1085 
 HIS   0.006   0.001   HIS A 618 
 PHE   0.022   0.001   PHE A 557 
 TYR   0.018   0.002   TYR A1064 
 ARG   0.002   0.000   ARG A 219 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 42
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  593 MET cc_start: 0.9573 (ppp) cc_final: 0.9343 (ppp)
REVERT: A  764 TYR cc_start: 0.9395 (m-80) cc_final: 0.9169 (m-80)
REVERT: A  786 GLU cc_start: 0.8140 (mp0) cc_final: 0.7696 (mp0)
REVERT: A  908 ASP cc_start: 0.8457 (t0) cc_final: 0.8174 (t0)
REVERT: A  938 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8692 (t80)
REVERT: A 1018 MET cc_start: 0.9171 (mtm) cc_final: 0.8839 (mtm)
REVERT: A 1199 ILE cc_start: 0.9638 (OUTLIER) cc_final: 0.9438 (mm)
REVERT: A 1280 HIS cc_start: 0.9301 (OUTLIER) cc_final: 0.8663 (t-90)
  outliers start: 29
  outliers final: 17
  residues processed: 70
  average time/residue: 0.2151
  time to fit residues: 22.7227
Evaluate side-chains
  56 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 36
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  755 HIS
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  938 PHE
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1199 ILE
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1247 VAL
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1280 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 42 optimal weight:    8.9990
   chunk 81 optimal weight:    9.9990
   chunk 92 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 104 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 GLN
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1143 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 = 0.3140 r_free = 0.3140 target = 0.040940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.027890 restraints weight = 78090.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.028880 restraints weight = 40870.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.029488 restraints weight = 28211.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.3457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  10640  Z= 0.396
  Angle     :  0.666   7.916  14806  Z= 0.363
  Chirality :  0.042   0.174   1641
  Planarity :  0.004   0.057   1559
  Dihedral  : 23.651 157.992   2279
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 24.41 %
    Favored  : 71.67 %
  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:  0.65 (0.28), residues: 991
  helix:  0.95 (0.24), residues: 449
  sheet: -0.63 (0.40), residues: 141
  loop :  0.46 (0.35), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A1085 
 HIS   0.007   0.001   HIS A 618 
 PHE   0.034   0.002   PHE A 999 
 TYR   0.017   0.002   TYR A  61 
 ARG   0.003   0.000   ARG A 912 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 35
  time to evaluate  : 1.187 
Fit side-chains
   revert: symmetry clash
REVERT: A  305 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8201 (mm)
REVERT: A  307 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7955 (tmmt)
REVERT: A  593 MET cc_start: 0.9519 (ppp) cc_final: 0.9191 (ppp)
REVERT: A  786 GLU cc_start: 0.8136 (mp0) cc_final: 0.7741 (mp0)
REVERT: A  938 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8692 (t80)
REVERT: A 1018 MET cc_start: 0.9150 (mtm) cc_final: 0.8794 (mtm)
REVERT: A 1199 ILE cc_start: 0.9593 (OUTLIER) cc_final: 0.9367 (mm)
REVERT: A 1280 HIS cc_start: 0.9255 (OUTLIER) cc_final: 0.8655 (t-90)
  outliers start: 35
  outliers final: 24
  residues processed: 68
  average time/residue: 0.2039
  time to fit residues: 21.4431
Evaluate side-chains
  62 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 33
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain A residue  624 THR
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  755 HIS
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  938 PHE
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1199 ILE
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1247 VAL
Chi-restraints excluded: chain A residue 1277 LEU
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1280 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 93 optimal weight:    8.9990
   chunk 7 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 98 optimal weight:    8.9990
   chunk 78 optimal weight:    0.0170
   chunk 80 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 83 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 100 optimal weight:   10.0000
   overall best weight:    1.3222

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

Flipped N/Q/H residues before XYZ refinement:
** A   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1143 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 = 0.3183 r_free = 0.3183 target = 0.042042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.029013 restraints weight = 74475.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.030076 restraints weight = 38212.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.030736 restraints weight = 25823.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10640  Z= 0.180
  Angle     :  0.608   8.923  14806  Z= 0.321
  Chirality :  0.040   0.210   1641
  Planarity :  0.004   0.056   1559
  Dihedral  : 23.447 155.957   2279
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 25.31 %
    Favored  : 71.56 %
  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:  0.85 (0.28), residues: 991
  helix:  1.21 (0.25), residues: 449
  sheet: -0.65 (0.39), residues: 158
  loop :  0.55 (0.36), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1085 
 HIS   0.005   0.001   HIS A 618 
 PHE   0.030   0.001   PHE A 999 
 TYR   0.013   0.002   TYR A 595 
 ARG   0.002   0.000   ARG A 219 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 38
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 GLU cc_start: 0.9107 (pp20) cc_final: 0.8713 (pp20)
REVERT: A  305 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7950 (mm)
REVERT: A  307 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7845 (tmmt)
REVERT: A  593 MET cc_start: 0.9592 (ppp) cc_final: 0.9270 (ppp)
REVERT: A  764 TYR cc_start: 0.9368 (m-80) cc_final: 0.9088 (m-80)
REVERT: A  786 GLU cc_start: 0.8108 (mp0) cc_final: 0.7783 (mp0)
REVERT: A  908 ASP cc_start: 0.8447 (t0) cc_final: 0.8000 (t0)
REVERT: A  938 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8664 (t80)
REVERT: A 1018 MET cc_start: 0.9119 (mtm) cc_final: 0.8889 (mtm)
REVERT: A 1199 ILE cc_start: 0.9613 (OUTLIER) cc_final: 0.9401 (mm)
REVERT: A 1280 HIS cc_start: 0.9329 (OUTLIER) cc_final: 0.8673 (t-90)
  outliers start: 28
  outliers final: 20
  residues processed: 65
  average time/residue: 0.2060
  time to fit residues: 20.4714
Evaluate side-chains
  62 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 37
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  755 HIS
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  938 PHE
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1023 LEU
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1199 ILE
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1247 VAL
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1280 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 74 optimal weight:    0.3980
   chunk 68 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 38 optimal weight:    0.6980
   chunk 69 optimal weight:    9.9990
   chunk 80 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 7 optimal weight:    2.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1143 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 = 0.3180 r_free = 0.3180 target = 0.041947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.028962 restraints weight = 75771.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.030008 restraints weight = 38904.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.030657 restraints weight = 26379.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10640  Z= 0.214
  Angle     :  0.608   8.692  14806  Z= 0.321
  Chirality :  0.040   0.195   1641
  Planarity :  0.004   0.058   1559
  Dihedral  : 23.419 155.424   2279
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 25.42 %
    Favored  : 71.67 %
  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:  0.91 (0.28), residues: 991
  helix:  1.29 (0.25), residues: 449
  sheet: -0.62 (0.39), residues: 158
  loop :  0.55 (0.36), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1085 
 HIS   0.005   0.001   HIS A 618 
 PHE   0.030   0.001   PHE A 999 
 TYR   0.015   0.001   TYR A1064 
 ARG   0.002   0.000   ARG A 947 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 38
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 GLU cc_start: 0.9100 (pp20) cc_final: 0.8712 (pp20)
REVERT: A  307 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7910 (tmmt)
REVERT: A  593 MET cc_start: 0.9559 (ppp) cc_final: 0.9244 (ppp)
REVERT: A  764 TYR cc_start: 0.9350 (m-80) cc_final: 0.9063 (m-80)
REVERT: A  786 GLU cc_start: 0.8092 (mp0) cc_final: 0.7807 (mp0)
REVERT: A  908 ASP cc_start: 0.8506 (t0) cc_final: 0.8040 (t0)
REVERT: A  938 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8653 (t80)
REVERT: A 1018 MET cc_start: 0.9093 (mtm) cc_final: 0.8847 (mtm)
REVERT: A 1199 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9346 (mm)
REVERT: A 1280 HIS cc_start: 0.9278 (OUTLIER) cc_final: 0.8628 (t-90)
  outliers start: 26
  outliers final: 20
  residues processed: 63
  average time/residue: 0.2172
  time to fit residues: 20.6575
Evaluate side-chains
  61 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 37
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  755 HIS
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  938 PHE
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1023 LEU
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1199 ILE
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1247 VAL
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1280 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 5 optimal weight:    0.7980
   chunk 93 optimal weight:    0.0770
   chunk 67 optimal weight:    3.9990
   chunk 80 optimal weight:    9.9990
   chunk 100 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9980
   overall best weight:    1.1742

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

Flipped N/Q/H residues before XYZ refinement:
** A   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1143 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 = 0.3196 r_free = 0.3196 target = 0.042668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.029620 restraints weight = 74997.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.030704 restraints weight = 38599.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.031381 restraints weight = 26027.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10640  Z= 0.171
  Angle     :  0.606   8.992  14806  Z= 0.315
  Chirality :  0.039   0.197   1641
  Planarity :  0.004   0.057   1559
  Dihedral  : 23.295 154.012   2279
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 25.76 %
    Favored  : 71.56 %
  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:  0.96 (0.28), residues: 991
  helix:  1.38 (0.25), residues: 449
  sheet: -0.57 (0.40), residues: 158
  loop :  0.49 (0.35), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1085 
 HIS   0.004   0.001   HIS A1096 
 PHE   0.029   0.001   PHE A 999 
 TYR   0.014   0.001   TYR A1043 
 ARG   0.002   0.000   ARG A 219 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 39
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 GLU cc_start: 0.9119 (pp20) cc_final: 0.8744 (pp20)
REVERT: A  307 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7907 (tmmt)
REVERT: A  593 MET cc_start: 0.9583 (ppp) cc_final: 0.9259 (ppp)
REVERT: A  764 TYR cc_start: 0.9359 (m-80) cc_final: 0.9102 (m-80)
REVERT: A  786 GLU cc_start: 0.8095 (mp0) cc_final: 0.7771 (mp0)
REVERT: A  908 ASP cc_start: 0.8455 (t0) cc_final: 0.8038 (t0)
REVERT: A  938 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8677 (t80)
REVERT: A 1199 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9360 (mm)
REVERT: A 1280 HIS cc_start: 0.9339 (OUTLIER) cc_final: 0.8692 (t-90)
  outliers start: 24
  outliers final: 19
  residues processed: 62
  average time/residue: 0.2074
  time to fit residues: 19.8925
Evaluate side-chains
  61 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 38
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  755 HIS
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  938 PHE
Chi-restraints excluded: chain A residue  989 VAL
Chi-restraints excluded: chain A residue 1023 LEU
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1199 ILE
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1247 VAL
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1280 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 89 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0060
   chunk 75 optimal weight:    0.9990
   chunk 95 optimal weight:    7.9990
   chunk 105 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 100 optimal weight:   10.0000
   chunk 104 optimal weight:    4.9990
   overall best weight:    1.7802

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

Flipped N/Q/H residues before XYZ refinement:
** A   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1143 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 = 0.3186 r_free = 0.3186 target = 0.042322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.029359 restraints weight = 74858.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.030423 restraints weight = 38759.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.031089 restraints weight = 26257.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10640  Z= 0.195
  Angle     :  0.604   9.005  14806  Z= 0.316
  Chirality :  0.039   0.192   1641
  Planarity :  0.004   0.057   1559
  Dihedral  : 23.306 154.058   2279
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 25.87 %
    Favored  : 71.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.28), residues: 991
  helix:  1.46 (0.25), residues: 449
  sheet: -0.54 (0.39), residues: 158
  loop :  0.51 (0.36), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1085 
 HIS   0.004   0.001   HIS A1096 
 PHE   0.029   0.001   PHE A 999 
 TYR   0.023   0.001   TYR A1064 
 ARG   0.002   0.000   ARG A 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2802.86 seconds
wall clock time: 51 minutes 32.78 seconds (3092.78 seconds total)