Starting phenix.real_space_refine
on Wed May 21 07:44:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yny_39431/05_2025/8yny_39431.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yny_39431/05_2025/8yny_39431.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yny_39431/05_2025/8yny_39431.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yny_39431/05_2025/8yny_39431.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yny_39431/05_2025/8yny_39431.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yny_39431/05_2025/8yny_39431.cif"
  }
  resolution = 4.52
  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=   0.003 sd=   0.094
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     386      5.49       5
     S      30      5.16       5
     C   12247      2.51       5
     N    3895      2.21       5
     O    4829      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 21387
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 743
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "B"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "C"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 743
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
    Chain: "D"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "E"
      Number of atoms: 738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 738
          Classifications: {'peptide': 90}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "F"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 741
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
    Chain: "H"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "I"
      Number of atoms: 2794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 2794
          Classifications: {'DNA': 137}
          Link IDs: {'rna3p': 136}
    Chain: "J"
      Number of atoms: 2783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 2783
          Classifications: {'DNA': 135}
          Link IDs: {'rna3p': 134}
    Chain: "K"
      Number of atoms: 351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 351
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
    Chain: "W"
      Number of atoms: 2072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 2072
          Classifications: {'RNA': 97}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 48, 'rna3p_pyr': 38}
          Link IDs: {'rna2p': 11, 'rna3p': 85}
    Chain: "X"
      Number of atoms: 7759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 941, 7759
          Classifications: {'peptide': 941}
          Link IDs: {'PTRANS': 26, 'TRANS': 914}
          Chain breaks: 13
  Time building chain proxies: 12.08, per 1000 atoms: 0.56
  Number of scatterers: 21387
  At special positions: 0
  Unit cell: (106.575, 115.71, 190.312, 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      30     16.00
     P     386     15.00
     O    4829      8.00
     N    3895      7.00
     C   12247      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: 5.42
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3126

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 8 sheets defined
      64.7% alpha, 5.1% beta
      167 base pairs and 277 stacking pairs defined.
    Time for finding SS restraints: 9.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.660A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 79
      removed outlier: 3.901A  pdb=" N   LEU A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.527A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 47 through 76
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.290A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.915A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 88 through 99
    Processing helix  chain 'D' and resid 103 through 121
    Processing helix  chain 'E' and resid 47 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.791A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.980A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ALA E 111 " --> pdb=" O   THR E 107 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ILE E 112 " --> pdb=" O   ASN E 108 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   HIS E 113 " --> pdb=" O   LEU E 109 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.544A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.619A  pdb=" N   GLY F  28 " --> pdb=" O   ASN F  25 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 47 through 77
      removed outlier: 3.798A  pdb=" N   TYR F  51 " --> pdb=" O   SER F  47 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   GLU F  52 " --> pdb=" O   GLY F  48 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 38
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.042A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 4.105A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   GLN G  84 " --> pdb=" O   PRO G  80 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 98
      removed outlier: 3.681A  pdb=" N   LEU G  96 " --> pdb=" O   GLU G  92 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 82
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.772A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 121
    Processing helix  chain 'X' and resid 59 through 91
      removed outlier: 4.512A  pdb=" N   ASN X  88 " --> pdb=" O   GLU X  84 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   GLU X  89 " --> pdb=" O   ILE X  85 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 95 through 104
      removed outlier: 3.733A  pdb=" N   HIS X  99 " --> pdb=" O   ASP X  95 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 121 through 132
      removed outlier: 3.552A  pdb=" N   GLU X 125 " --> pdb=" O   ASN X 121 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 134 through 145
      removed outlier: 3.795A  pdb=" N   LEU X 138 " --> pdb=" O   THR X 134 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 150 through 164
    Processing helix  chain 'X' and resid 315 through 343
      removed outlier: 3.789A  pdb=" N   ALA X 319 " --> pdb=" O   ALA X 315 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 343 through 353
      removed outlier: 3.819A  pdb=" N   ASP X 353 " --> pdb=" O   GLU X 349 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 358 through 364
    Processing helix  chain 'X' and resid 368 through 383
      Proline residue:  X 378  - end of helix
    Processing helix  chain 'X' and resid 387 through 395
    Processing helix  chain 'X' and resid 405 through 410
      removed outlier: 4.158A  pdb=" N   GLY X 408 " --> pdb=" O   PHE X 405 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 411 through 427
      removed outlier: 4.204A  pdb=" N   HIS X 415 " --> pdb=" O   PRO X 411 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 430 through 436
    Processing helix  chain 'X' and resid 436 through 446
    Processing helix  chain 'X' and resid 477 through 482
    Processing helix  chain 'X' and resid 483 through 494
    Processing helix  chain 'X' and resid 512 through 525
    Processing helix  chain 'X' and resid 591 through 598
    Processing helix  chain 'X' and resid 614 through 626
    Processing helix  chain 'X' and resid 628 through 637
    Processing helix  chain 'X' and resid 644 through 654
    Processing helix  chain 'X' and resid 663 through 668
    Processing helix  chain 'X' and resid 679 through 685
    Processing helix  chain 'X' and resid 692 through 698
    Processing helix  chain 'X' and resid 702 through 709
      removed outlier: 4.070A  pdb=" N   GLU X 706 " --> pdb=" O   LEU X 702 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 720 through 727
    Processing helix  chain 'X' and resid 730 through 751
    Processing helix  chain 'X' and resid 926 through 940
    Processing helix  chain 'X' and resid 959 through 971
      removed outlier: 3.637A  pdb=" N   VAL X 963 " --> pdb=" O   LYS X 959 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 980 through 999
      removed outlier: 3.701A  pdb=" N   ALA X 987 " --> pdb=" O   HIS X 983 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   TYR X 988 " --> pdb=" O   ALA X 984 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLY X 994 " --> pdb=" O   ASN X 990 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 1001 through 1007
    Processing helix  chain 'X' and resid 1041 through 1047
      removed outlier: 4.248A  pdb=" N   PHE X1045 " --> pdb=" O   ILE X1042 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LYS X1047 " --> pdb=" O   ASN X1044 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 1077 through 1089
    Processing helix  chain 'X' and resid 1127 through 1132
    Processing helix  chain 'X' and resid 1168 through 1177
      removed outlier: 4.160A  pdb=" N   SER X1172 " --> pdb=" O   ILE X1168 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   SER X1173 " --> pdb=" O   MET X1169 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 1177 through 1185
    Processing helix  chain 'X' and resid 1191 through 1195
    Processing helix  chain 'X' and resid 1229 through 1241
    Processing helix  chain 'X' and resid 1254 through 1262
    Processing helix  chain 'X' and resid 1262 through 1281
    Processing helix  chain 'X' and resid 1283 through 1298
      removed outlier: 3.617A  pdb=" N   LEU X1287 " --> pdb=" O   ALA X1283 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 1301 through 1313
    Processing helix  chain 'X' and resid 1314 through 1316
      No H-bonds generated for 'chain 'X' and resid 1314 through 1316'
    Processing helix  chain 'X' and resid 1339 through 1345
      removed outlier: 3.678A  pdb=" N   ASP X1344 " --> pdb=" O   LYS X1340 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.982A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA3, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA4, first strand: chain 'X' and resid 954 through 957
      removed outlier: 4.168A  pdb=" N   ASN X 758 " --> pdb=" O   TYR X   5 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'X' and resid 29 through 33
    Processing sheet with id=AA6, first strand: chain 'X' and resid 1156 through 1167
      removed outlier: 5.704A  pdb=" N   LYS X1156 " --> pdb=" O   GLU X1150 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLU X1150 " --> pdb=" O   LYS X1156 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   LYS X1158 " --> pdb=" O   LYS X1148 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LYS X1148 " --> pdb=" O   LYS X1158 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL X1160 " --> pdb=" O   VAL X1146 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   VAL X1146 " --> pdb=" O   VAL X1160 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   GLU X1162 " --> pdb=" O   LEU X1144 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   LEU X1144 " --> pdb=" O   GLU X1162 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   LEU X1164 " --> pdb=" O   SER X1142 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   SER X1142 " --> pdb=" O   LEU X1164 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   ILE X1166 " --> pdb=" O   ALA X1140 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ILE X1196 " --> pdb=" O   LEU X1144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'X' and resid 1220 through 1222
      removed outlier: 3.841A  pdb=" N   SER X1202 " --> pdb=" O   LEU X1214 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   LEU X1203 " --> pdb=" O   ILE X1348 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ILE X1348 " --> pdb=" O   LEU X1203 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   GLU X1205 " --> pdb=" O   THR X1346 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   THR X1346 " --> pdb=" O   GLU X1205 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'X' and resid 1324 through 1325

    761 hydrogen bonds defined for protein.
    2256 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      431 hydrogen bonds
      854 hydrogen bond angles
      0 basepair planarities
      167 basepair parallelities
      277 stacking parallelities
  Total time for adding SS restraints: 12.65

  Time building geometry restraints manager: 6.36 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: 4252
        1.33 -     1.45: 6775
        1.45 -     1.57: 10716
        1.57 -     1.69: 768
        1.69 -     1.81: 55
  Bond restraints: 22566
  Sorted by residual:
  bond pdb=" N   ILE D  86 "
       pdb=" CA  ILE D  86 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.22e-02 6.72e+03 7.84e+00
  bond pdb=" P    DG I  28 "
       pdb=" OP2  DG I  28 "
    ideal  model  delta    sigma   weight residual
    1.480  1.523 -0.043 2.00e-02 2.50e+03 4.67e+00
  bond pdb=" P    DG J  21 "
       pdb=" OP1  DG J  21 "
    ideal  model  delta    sigma   weight residual
    1.480  1.522 -0.042 2.00e-02 2.50e+03 4.40e+00
  bond pdb=" P    DC I   9 "
       pdb=" OP2  DC I   9 "
    ideal  model  delta    sigma   weight residual
    1.480  1.521 -0.041 2.00e-02 2.50e+03 4.30e+00
  bond pdb=" P    DC J  67 "
       pdb=" OP2  DC J  67 "
    ideal  model  delta    sigma   weight residual
    1.480  1.521 -0.041 2.00e-02 2.50e+03 4.28e+00
  ... (remaining 22561 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 31364
        2.25 -     4.51: 616
        4.51 -     6.76: 123
        6.76 -     9.01: 26
        9.01 -    11.26: 4
  Bond angle restraints: 32133
  Sorted by residual:
  angle pdb=" O3'  DT I  17 "
        pdb=" P    DC I  18 "
        pdb=" O5'  DC I  18 "
      ideal   model   delta    sigma   weight residual
     104.00   95.46    8.54 1.50e+00 4.44e-01 3.24e+01
  angle pdb=" O3'  DG J  20 "
        pdb=" P    DG J  21 "
        pdb=" O5'  DG J  21 "
      ideal   model   delta    sigma   weight residual
     104.00   96.07    7.93 1.50e+00 4.44e-01 2.80e+01
  angle pdb=" O3'  DC I  18 "
        pdb=" P    DC I  19 "
        pdb=" O5'  DC I  19 "
      ideal   model   delta    sigma   weight residual
     104.00   97.07    6.93 1.50e+00 4.44e-01 2.13e+01
  angle pdb=" O3'  DC I  19 "
        pdb=" P    DG I  20 "
        pdb=" O5'  DG I  20 "
      ideal   model   delta    sigma   weight residual
     104.00   97.43    6.57 1.50e+00 4.44e-01 1.92e+01
  angle pdb=" O3'  DC I  30 "
        pdb=" P    DC I  31 "
        pdb=" O5'  DC I  31 "
      ideal   model   delta    sigma   weight residual
     104.00   97.47    6.53 1.50e+00 4.44e-01 1.90e+01
  ... (remaining 32128 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.57: 10809
       31.57 -    63.13: 1977
       63.13 -    94.70: 143
       94.70 -   126.27: 11
      126.27 -   157.84: 4
  Dihedral angle restraints: 12944
    sinusoidal: 8120
      harmonic: 4824
  Sorted by residual:
  dihedral pdb=" CA  TYR F  98 "
           pdb=" C   TYR F  98 "
           pdb=" N   GLY F  99 "
           pdb=" CA  GLY F  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.07   26.93     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" C4'   A W  28 "
           pdb=" O4'   A W  28 "
           pdb=" C1'   A W  28 "
           pdb=" C2'   A W  28 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -21.00    7.49  -28.49     1      8.00e+00 1.56e-02 1.82e+01
  dihedral pdb=" C3'   A W  28 "
           pdb=" C4'   A W  28 "
           pdb=" O4'   A W  28 "
           pdb=" C1'   A W  28 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -2.00  -28.60   26.60     1      8.00e+00 1.56e-02 1.59e+01
  ... (remaining 12941 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 3630
       0.122 -    0.244: 23
       0.244 -    0.366: 0
       0.366 -    0.488: 4
       0.488 -    0.610: 45
  Chirality restraints: 3702
  Sorted by residual:
  chirality pdb=" P    DG I  28 "
            pdb=" OP1  DG I  28 "
            pdb=" OP2  DG I  28 "
            pdb=" O5'  DG I  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.96   -0.61 2.00e-01 2.50e+01 9.30e+00
  chirality pdb=" P    DG I  47 "
            pdb=" OP1  DG I  47 "
            pdb=" OP2  DG I  47 "
            pdb=" O5'  DG I  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.95   -0.61 2.00e-01 2.50e+01 9.26e+00
  chirality pdb=" P    DT J  68 "
            pdb=" OP1  DT J  68 "
            pdb=" OP2  DT J  68 "
            pdb=" O5'  DT J  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.95   -0.61 2.00e-01 2.50e+01 9.20e+00
  ... (remaining 3699 not shown)

  Planarity restraints: 2702
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I 100 "    0.006 2.00e-02 2.50e+03   2.71e-02 1.65e+01
        pdb=" N1   DC I 100 "   -0.010 2.00e-02 2.50e+03
        pdb=" C2   DC I 100 "    0.068 2.00e-02 2.50e+03
        pdb=" O2   DC I 100 "   -0.033 2.00e-02 2.50e+03
        pdb=" N3   DC I 100 "   -0.023 2.00e-02 2.50e+03
        pdb=" C4   DC I 100 "    0.000 2.00e-02 2.50e+03
        pdb=" N4   DC I 100 "    0.008 2.00e-02 2.50e+03
        pdb=" C5   DC I 100 "   -0.010 2.00e-02 2.50e+03
        pdb=" C6   DC I 100 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J -18 "   -0.020 2.00e-02 2.50e+03   1.57e-02 7.37e+00
        pdb=" N9   DG J -18 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DG J -18 "    0.006 2.00e-02 2.50e+03
        pdb=" N7   DG J -18 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DG J -18 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG J -18 "   -0.005 2.00e-02 2.50e+03
        pdb=" O6   DG J -18 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DG J -18 "    0.012 2.00e-02 2.50e+03
        pdb=" C2   DG J -18 "   -0.035 2.00e-02 2.50e+03
        pdb=" N2   DG J -18 "    0.023 2.00e-02 2.50e+03
        pdb=" N3   DG J -18 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DG J -18 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J  38 "   -0.034 2.00e-02 2.50e+03   1.53e-02 7.03e+00
        pdb=" N9   DG J  38 "    0.038 2.00e-02 2.50e+03
        pdb=" C8   DG J  38 "    0.006 2.00e-02 2.50e+03
        pdb=" N7   DG J  38 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG J  38 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DG J  38 "   -0.008 2.00e-02 2.50e+03
        pdb=" O6   DG J  38 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1   DG J  38 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG J  38 "    0.005 2.00e-02 2.50e+03
        pdb=" N2   DG J  38 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DG J  38 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DG J  38 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 2699 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.74: 2067
        2.74 -     3.28: 23061
        3.28 -     3.82: 43980
        3.82 -     4.36: 50281
        4.36 -     4.90: 70903
  Nonbonded interactions: 190292
  Sorted by model distance:
  nonbonded pdb=" O2'   C W   8 "
            pdb=" OP1   C W   9 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O2'   A W  42 "
            pdb=" OP1   G W  43 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" NH1 ARG E 116 "
            pdb=" OP2  DC J  -2 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" O   ALA X 149 "
            pdb=" OH  TYR X 430 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OP1   G W  16 "
            pdb=" NH2 ARG X  74 "
     model   vdw
     2.213 3.120
  ... (remaining 190287 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 46 through 134)
  selection = (chain 'E' and resid 46 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 16 through 109)
  selection = (chain 'G' and resid 16 through 109)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.430
  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:             0.020
  Extract box with map and model:          0.850
  Check model and map are aligned:         0.160
  Set scattering table:                    0.210
  Process input model:                     56.850
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
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   0.051  22566  Z= 0.234
  Angle     :  0.815  11.263  32133  Z= 0.440
  Chirality :  0.073   0.610   3702
  Planarity :  0.004   0.043   2702
  Dihedral  : 25.386 157.836   9818
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 24.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  7.49 %
    Favored  : 92.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.20), residues: 1609
  helix:  1.07 (0.16), residues: 942
  sheet:  0.09 (0.59), residues: 75
  loop : -0.67 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP X 464 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.013   0.002   PHE X1313 
 TYR   0.016   0.002   TYR C  57 
 ARG   0.006   0.001   ARG X1210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13676 ( 1192)
  hydrogen bonds       : angle       6.24768 ( 3110)
  covalent geometry    : bond        0.00488 (22566)
  covalent geometry    : angle       0.81519 (32133)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 1.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 99
  average time/residue: 0.3699
  time to fit residues: 56.9413
Evaluate side-chains
  53 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 1.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 168 optimal weight:    7.9990
   chunk 150 optimal weight:    4.9990
   chunk 83 optimal weight:   30.0000
   chunk 51 optimal weight:   20.0000
   chunk 101 optimal weight:   20.0000
   chunk 80 optimal weight:   10.0000
   chunk 155 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 94 optimal weight:    8.9990
   chunk 116 optimal weight:    5.9990
   chunk 180 optimal weight:   10.0000
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
G  24 GLN
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X  14 ASN
X 129 HIS
X 415 HIS
X 459 ASN
** X 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X1234 ASN
X1256 GLN
** X1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.034365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.028143 restraints weight = 380713.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.028706 restraints weight = 253015.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.029062 restraints weight = 191000.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  22566  Z= 0.261
  Angle     :  0.719  10.837  32133  Z= 0.405
  Chirality :  0.041   0.238   3702
  Planarity :  0.005   0.059   2702
  Dihedral  : 29.651 174.551   6426
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 23.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.96 %
    Favored  : 95.91 %
  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 (0.20), residues: 1609
  helix:  1.17 (0.16), residues: 1021
  sheet: -0.48 (0.50), residues: 90
  loop : -0.73 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP X 464 
 HIS   0.006   0.002   HIS F  75 
 PHE   0.018   0.002   PHE X 626 
 TYR   0.019   0.002   TYR X1232 
 ARG   0.008   0.001   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08508 ( 1192)
  hydrogen bonds       : angle       4.54746 ( 3110)
  covalent geometry    : bond        0.00547 (22566)
  covalent geometry    : angle       0.71910 (32133)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 1.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9175 (t80) cc_final: 0.8770 (t80)
REVERT: A   90 MET cc_start: 0.9434 (mmp) cc_final: 0.9173 (mmm)
REVERT: D  105 LYS cc_start: 0.9554 (pttm) cc_final: 0.9329 (mptt)
REVERT: D  106 HIS cc_start: 0.9582 (m90) cc_final: 0.9329 (m90)
REVERT: H   59 MET cc_start: 0.9743 (mmm) cc_final: 0.9492 (mmm)
REVERT: H   68 GLU cc_start: 0.9261 (tt0) cc_final: 0.9012 (tm-30)
REVERT: H   77 LEU cc_start: 0.9731 (tt) cc_final: 0.9528 (pp)
REVERT: H   79 HIS cc_start: 0.9537 (m90) cc_final: 0.9197 (m90)
REVERT: X  751 MET cc_start: 0.9184 (ttm) cc_final: 0.8940 (ttp)
REVERT: X 1169 MET cc_start: 0.9609 (ttm) cc_final: 0.9086 (tpp)
  outliers start: 2
  outliers final: 0
  residues processed: 70
  average time/residue: 0.3290
  time to fit residues: 37.5225
Evaluate side-chains
  53 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 1.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 181 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   chunk 148 optimal weight:    9.9990
   chunk 142 optimal weight:   20.0000
   chunk 158 optimal weight:   30.0000
   chunk 1 optimal weight:    9.9990
   chunk 14 optimal weight:   20.0000
   chunk 150 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 197 optimal weight:   10.0000
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 692 ASN
X 723 HIS
** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X1317 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.034542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.028245 restraints weight = 377580.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.028825 restraints weight = 247608.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.029128 restraints weight = 185663.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081  22566  Z= 0.193
  Angle     :  0.619   7.280  32133  Z= 0.353
  Chirality :  0.037   0.200   3702
  Planarity :  0.004   0.054   2702
  Dihedral  : 29.420 166.902   6426
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.05 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  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:  1.09 (0.21), residues: 1609
  helix:  1.52 (0.16), residues: 1016
  sheet: -0.50 (0.50), residues: 88
  loop : -0.62 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP X 464 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.016   0.002   PHE C  25 
 TYR   0.018   0.002   TYR X 347 
 ARG   0.005   0.000   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05737 ( 1192)
  hydrogen bonds       : angle       4.13785 ( 3110)
  covalent geometry    : bond        0.00405 (22566)
  covalent geometry    : angle       0.61897 (32133)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9207 (t80) cc_final: 0.8976 (t80)
REVERT: A   90 MET cc_start: 0.9389 (mmp) cc_final: 0.9151 (mmm)
REVERT: D   68 GLU cc_start: 0.9608 (mm-30) cc_final: 0.9365 (mm-30)
REVERT: D  105 LYS cc_start: 0.9546 (pttm) cc_final: 0.9334 (ptpp)
REVERT: D  106 HIS cc_start: 0.9621 (m90) cc_final: 0.9393 (m90)
REVERT: G  102 ILE cc_start: 0.7248 (mp) cc_final: 0.6840 (tt)
REVERT: H   68 GLU cc_start: 0.9260 (tt0) cc_final: 0.9025 (tm-30)
REVERT: H   77 LEU cc_start: 0.9744 (tt) cc_final: 0.9491 (pp)
REVERT: X  383 MET cc_start: 0.9039 (ttm) cc_final: 0.8658 (ttm)
REVERT: X  419 LEU cc_start: 0.9620 (tt) cc_final: 0.9367 (mt)
REVERT: X 1169 MET cc_start: 0.9597 (ttm) cc_final: 0.9097 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.3407
  time to fit residues: 35.9785
Evaluate side-chains
  53 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 1.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 0 optimal weight:   40.0000
   chunk 37 optimal weight:    3.9990
   chunk 168 optimal weight:   20.0000
   chunk 97 optimal weight:   20.0000
   chunk 181 optimal weight:    0.8980
   chunk 69 optimal weight:   10.0000
   chunk 52 optimal weight:   30.0000
   chunk 79 optimal weight:   10.0000
   chunk 113 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    6.3790

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  24 GLN
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X1297 HIS
X1308 ASN
X1311 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.032943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.026751 restraints weight = 394513.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.027320 restraints weight = 261885.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.027680 restraints weight = 196156.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.3878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  22566  Z= 0.239
  Angle     :  0.652   8.174  32133  Z= 0.371
  Chirality :  0.039   0.227   3702
  Planarity :  0.005   0.060   2702
  Dihedral  : 29.760 177.803   6426
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 23.05
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.73 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  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:  1.01 (0.20), residues: 1609
  helix:  1.43 (0.16), residues: 1010
  sheet: -0.93 (0.52), residues: 90
  loop : -0.47 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP X 464 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.015   0.002   PHE X 498 
 TYR   0.020   0.002   TYR H  39 
 ARG   0.007   0.001   ARG X 586 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07985 ( 1192)
  hydrogen bonds       : angle       4.32052 ( 3110)
  covalent geometry    : bond        0.00497 (22566)
  covalent geometry    : angle       0.65161 (32133)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9247 (t80) cc_final: 0.8848 (t80)
REVERT: A   90 MET cc_start: 0.9448 (mmp) cc_final: 0.9107 (mmm)
REVERT: D   59 MET cc_start: 0.9826 (mmp) cc_final: 0.9623 (mmm)
REVERT: D  106 HIS cc_start: 0.9638 (m90) cc_final: 0.9372 (m90)
REVERT: E   67 PHE cc_start: 0.9316 (t80) cc_final: 0.9095 (t80)
REVERT: G  102 ILE cc_start: 0.7442 (mp) cc_final: 0.7097 (tt)
REVERT: H   68 GLU cc_start: 0.9182 (tt0) cc_final: 0.8922 (tm-30)
REVERT: H   77 LEU cc_start: 0.9613 (tt) cc_final: 0.9282 (pp)
REVERT: X  383 MET cc_start: 0.9296 (ttm) cc_final: 0.8786 (ttm)
REVERT: X  751 MET cc_start: 0.9080 (ttm) cc_final: 0.8606 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.3240
  time to fit residues: 31.9107
Evaluate side-chains
  50 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 1.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 64 optimal weight:   20.0000
   chunk 180 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 79 optimal weight:   10.0000
   chunk 32 optimal weight:    8.9990
   chunk 130 optimal weight:    8.9990
   chunk 72 optimal weight:   10.0000
   chunk 162 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 119 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
H  60 ASN
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.033406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.027155 restraints weight = 385512.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.027731 restraints weight = 251750.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.028095 restraints weight = 186912.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  22566  Z= 0.193
  Angle     :  0.612   8.116  32133  Z= 0.348
  Chirality :  0.037   0.208   3702
  Planarity :  0.004   0.058   2702
  Dihedral  : 29.569 176.639   6426
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 19.08
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.49 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  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:  1.16 (0.21), residues: 1609
  helix:  1.61 (0.16), residues: 1005
  sheet: -1.31 (0.51), residues: 93
  loop : -0.41 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP X 464 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.012   0.001   PHE X 462 
 TYR   0.013   0.001   TYR X1336 
 ARG   0.004   0.000   ARG X1210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05981 ( 1192)
  hydrogen bonds       : angle       4.15046 ( 3110)
  covalent geometry    : bond        0.00402 (22566)
  covalent geometry    : angle       0.61240 (32133)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 1.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9207 (t80) cc_final: 0.8791 (t80)
REVERT: A   90 MET cc_start: 0.9364 (mmp) cc_final: 0.9046 (mmp)
REVERT: D   59 MET cc_start: 0.9829 (mmp) cc_final: 0.9615 (mmm)
REVERT: D   68 GLU cc_start: 0.9652 (mm-30) cc_final: 0.9367 (mm-30)
REVERT: D  106 HIS cc_start: 0.9635 (m90) cc_final: 0.9384 (m90)
REVERT: E   67 PHE cc_start: 0.9320 (t80) cc_final: 0.9090 (t80)
REVERT: G  102 ILE cc_start: 0.7350 (mp) cc_final: 0.6944 (tt)
REVERT: H   68 GLU cc_start: 0.9187 (tt0) cc_final: 0.8935 (tm-30)
REVERT: H   77 LEU cc_start: 0.9596 (tt) cc_final: 0.9300 (pp)
REVERT: H   79 HIS cc_start: 0.9471 (m90) cc_final: 0.9125 (m90)
REVERT: X  383 MET cc_start: 0.9363 (ttm) cc_final: 0.9153 (ttm)
REVERT: X  419 LEU cc_start: 0.9575 (tt) cc_final: 0.9319 (mt)
REVERT: X  751 MET cc_start: 0.9081 (ttm) cc_final: 0.8591 (ttm)
REVERT: X  939 MET cc_start: 0.8310 (tmm) cc_final: 0.8090 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.3054
  time to fit residues: 31.6947
Evaluate side-chains
  51 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 1.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 96 optimal weight:   30.0000
   chunk 189 optimal weight:   10.0000
   chunk 178 optimal weight:   30.0000
   chunk 185 optimal weight:    1.9990
   chunk 195 optimal weight:    7.9990
   chunk 184 optimal weight:    8.9990
   chunk 48 optimal weight:    9.9990
   chunk 27 optimal weight:   20.0000
   chunk 152 optimal weight:   20.0000
   chunk 128 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  60 ASN
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.032952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.026785 restraints weight = 387764.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.027360 restraints weight = 252302.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.027705 restraints weight = 187791.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  22566  Z= 0.206
  Angle     :  0.621   9.543  32133  Z= 0.353
  Chirality :  0.037   0.216   3702
  Planarity :  0.004   0.061   2702
  Dihedral  : 29.593 179.032   6426
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 20.70
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.61 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  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:  1.19 (0.21), residues: 1609
  helix:  1.60 (0.16), residues: 1004
  sheet: -0.85 (0.54), residues: 86
  loop : -0.43 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP X 464 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.021   0.002   PHE A  78 
 TYR   0.014   0.002   TYR X 515 
 ARG   0.013   0.000   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06708 ( 1192)
  hydrogen bonds       : angle       4.23933 ( 3110)
  covalent geometry    : bond        0.00430 (22566)
  covalent geometry    : angle       0.62062 (32133)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9235 (t80) cc_final: 0.8854 (t80)
REVERT: A   90 MET cc_start: 0.9398 (mmp) cc_final: 0.9067 (mmm)
REVERT: D   68 GLU cc_start: 0.9648 (mm-30) cc_final: 0.9374 (mm-30)
REVERT: D  106 HIS cc_start: 0.9647 (m90) cc_final: 0.9410 (m90)
REVERT: G  102 ILE cc_start: 0.6912 (mp) cc_final: 0.6434 (tt)
REVERT: H   68 GLU cc_start: 0.9150 (tt0) cc_final: 0.8926 (tm-30)
REVERT: H   77 LEU cc_start: 0.9798 (tt) cc_final: 0.9533 (pp)
REVERT: H   79 HIS cc_start: 0.9477 (m90) cc_final: 0.9124 (m90)
REVERT: X  383 MET cc_start: 0.9345 (ttm) cc_final: 0.8895 (ttm)
REVERT: X  751 MET cc_start: 0.9087 (ttm) cc_final: 0.8579 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.3029
  time to fit residues: 29.6460
Evaluate side-chains
  48 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 1.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 110 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 68 optimal weight:   20.0000
   chunk 82 optimal weight:   30.0000
   chunk 189 optimal weight:    4.9990
   chunk 170 optimal weight:    4.9990
   chunk 100 optimal weight:   20.0000
   chunk 19 optimal weight:    2.9990
   chunk 191 optimal weight:    7.9990
   chunk 184 optimal weight:    1.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  60 ASN
X 402 GLN
X 412 HIS
X 698 HIS
** X 983 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 = 0.3093 r_free = 0.3093 target = 0.033496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.027231 restraints weight = 381630.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.027843 restraints weight = 248267.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.028194 restraints weight = 182945.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.4705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  22566  Z= 0.169
  Angle     :  0.607  12.467  32133  Z= 0.342
  Chirality :  0.037   0.213   3702
  Planarity :  0.004   0.061   2702
  Dihedral  : 29.364 178.896   6426
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 17.83
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.36 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  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:  1.36 (0.21), residues: 1609
  helix:  1.74 (0.16), residues: 1004
  sheet: -1.00 (0.58), residues: 78
  loop : -0.37 (0.27), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP X1074 
 HIS   0.006   0.001   HIS A 113 
 PHE   0.013   0.001   PHE E  67 
 TYR   0.013   0.001   TYR X1336 
 ARG   0.009   0.000   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05128 ( 1192)
  hydrogen bonds       : angle       4.08653 ( 3110)
  covalent geometry    : bond        0.00354 (22566)
  covalent geometry    : angle       0.60699 (32133)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 1.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9181 (t80) cc_final: 0.8719 (t80)
REVERT: A   90 MET cc_start: 0.9415 (mmp) cc_final: 0.9125 (mmp)
REVERT: D   68 GLU cc_start: 0.9695 (mm-30) cc_final: 0.9406 (mm-30)
REVERT: D  106 HIS cc_start: 0.9662 (m90) cc_final: 0.9428 (m90)
REVERT: G  102 ILE cc_start: 0.6776 (mp) cc_final: 0.6338 (tt)
REVERT: H   68 GLU cc_start: 0.9109 (tt0) cc_final: 0.8878 (tm-30)
REVERT: H   77 LEU cc_start: 0.9814 (tt) cc_final: 0.9554 (pp)
REVERT: X  383 MET cc_start: 0.9319 (ttm) cc_final: 0.9058 (ttm)
REVERT: X  751 MET cc_start: 0.9285 (ttm) cc_final: 0.8852 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.3301
  time to fit residues: 32.7675
Evaluate side-chains
  49 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 1.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 65 optimal weight:    8.9990
   chunk 68 optimal weight:    8.9990
   chunk 88 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 142 optimal weight:    6.9990
   chunk 0 optimal weight:   40.0000
   chunk 81 optimal weight:   30.0000
   chunk 166 optimal weight:    0.9990
   chunk 110 optimal weight:    8.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  60 ASN
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.032989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.026735 restraints weight = 387172.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.027318 restraints weight = 251885.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.027668 restraints weight = 186648.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.5021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  22566  Z= 0.192
  Angle     :  0.612  12.022  32133  Z= 0.346
  Chirality :  0.037   0.222   3702
  Planarity :  0.004   0.060   2702
  Dihedral  : 29.425 179.670   6426
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.67 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  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:  1.34 (0.21), residues: 1609
  helix:  1.71 (0.16), residues: 1006
  sheet: -0.96 (0.59), residues: 78
  loop : -0.37 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP X 464 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.018   0.002   PHE X 688 
 TYR   0.014   0.002   TYR X 521 
 ARG   0.009   0.000   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06005 ( 1192)
  hydrogen bonds       : angle       4.16681 ( 3110)
  covalent geometry    : bond        0.00402 (22566)
  covalent geometry    : angle       0.61157 (32133)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 1.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9240 (t80) cc_final: 0.8795 (t80)
REVERT: A   78 PHE cc_start: 0.9400 (t80) cc_final: 0.9174 (t80)
REVERT: A   90 MET cc_start: 0.9416 (mmp) cc_final: 0.9107 (mmp)
REVERT: D   68 GLU cc_start: 0.9708 (mm-30) cc_final: 0.9450 (mm-30)
REVERT: E   67 PHE cc_start: 0.9332 (t80) cc_final: 0.9122 (t80)
REVERT: G  102 ILE cc_start: 0.6956 (mp) cc_final: 0.6393 (tt)
REVERT: H   68 GLU cc_start: 0.9196 (tt0) cc_final: 0.8976 (tm-30)
REVERT: H   77 LEU cc_start: 0.9817 (tt) cc_final: 0.9556 (pp)
REVERT: X  383 MET cc_start: 0.9342 (ttm) cc_final: 0.9078 (ttm)
REVERT: X  694 MET cc_start: 0.7316 (tmm) cc_final: 0.6934 (tmm)
REVERT: X  751 MET cc_start: 0.9276 (ttm) cc_final: 0.8825 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.3183
  time to fit residues: 29.1906
Evaluate side-chains
  47 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 104 optimal weight:   40.0000
   chunk 83 optimal weight:   30.0000
   chunk 55 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 171 optimal weight:    5.9990
   chunk 191 optimal weight:    6.9990
   chunk 185 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   chunk 146 optimal weight:   50.0000
   chunk 77 optimal weight:   10.0000
   overall best weight:    7.1992

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  60 ASN
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.031933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.025775 restraints weight = 395267.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.026361 restraints weight = 255883.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.026699 restraints weight = 189057.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.5521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  22566  Z= 0.253
  Angle     :  0.674  11.811  32133  Z= 0.379
  Chirality :  0.039   0.229   3702
  Planarity :  0.005   0.061   2702
  Dihedral  : 29.825 178.846   6426
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 25.74
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.05 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.21), residues: 1609
  helix:  1.49 (0.16), residues: 997
  sheet: -1.18 (0.59), residues: 78
  loop : -0.43 (0.27), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP X 464 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.017   0.002   PHE E  67 
 TYR   0.018   0.002   TYR G  39 
 ARG   0.007   0.001   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08103 ( 1192)
  hydrogen bonds       : angle       4.44242 ( 3110)
  covalent geometry    : bond        0.00525 (22566)
  covalent geometry    : angle       0.67392 (32133)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 1.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9281 (t80) cc_final: 0.8871 (t80)
REVERT: D   68 GLU cc_start: 0.9692 (mm-30) cc_final: 0.9441 (mm-30)
REVERT: E   67 PHE cc_start: 0.9199 (t80) cc_final: 0.8928 (t80)
REVERT: H   68 GLU cc_start: 0.9079 (tt0) cc_final: 0.8878 (tm-30)
REVERT: H   77 LEU cc_start: 0.9746 (tt) cc_final: 0.9478 (pp)
REVERT: H   79 HIS cc_start: 0.9493 (m90) cc_final: 0.9156 (m90)
REVERT: X  694 MET cc_start: 0.7261 (tmm) cc_final: 0.6578 (tmm)
REVERT: X  751 MET cc_start: 0.9287 (ttm) cc_final: 0.8873 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.3247
  time to fit residues: 30.2364
Evaluate side-chains
  44 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 129 optimal weight:    0.8980
   chunk 137 optimal weight:    9.9990
   chunk 73 optimal weight:   10.0000
   chunk 63 optimal weight:    7.9990
   chunk 164 optimal weight:   20.0000
   chunk 48 optimal weight:    0.9980
   chunk 188 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 93 optimal weight:   10.0000
   chunk 143 optimal weight:    8.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  46 HIS
X 342 GLN
X 983 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.033519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.027163 restraints weight = 380168.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.027770 restraints weight = 244889.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.028142 restraints weight = 179911.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.5565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  22566  Z= 0.157
  Angle     :  0.608  10.005  32133  Z= 0.341
  Chirality :  0.037   0.246   3702
  Planarity :  0.004   0.059   2702
  Dihedral  : 29.313 179.069   6426
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.30 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.07 %
    Favored  : 99.93 %
  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:  1.34 (0.21), residues: 1609
  helix:  1.75 (0.16), residues: 996
  sheet: -1.21 (0.57), residues: 83
  loop : -0.33 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP X 464 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.015   0.001   PHE A  78 
 TYR   0.017   0.001   TYR X 359 
 ARG   0.007   0.000   ARG X 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04643 ( 1192)
  hydrogen bonds       : angle       4.08739 ( 3110)
  covalent geometry    : bond        0.00334 (22566)
  covalent geometry    : angle       0.60785 (32133)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9208 (t80) cc_final: 0.8781 (t80)
REVERT: D   68 GLU cc_start: 0.9703 (mm-30) cc_final: 0.9448 (mm-30)
REVERT: E   67 PHE cc_start: 0.9314 (t80) cc_final: 0.9099 (t80)
REVERT: G  102 ILE cc_start: 0.6707 (mp) cc_final: 0.6069 (tt)
REVERT: H   66 ILE cc_start: 0.9260 (pt) cc_final: 0.9055 (pt)
REVERT: H   68 GLU cc_start: 0.9103 (tt0) cc_final: 0.8869 (tm-30)
REVERT: H   77 LEU cc_start: 0.9794 (tt) cc_final: 0.9539 (pp)
REVERT: X  694 MET cc_start: 0.6828 (tmm) cc_final: 0.6510 (tmm)
REVERT: X  751 MET cc_start: 0.9250 (ttm) cc_final: 0.8797 (ttm)
REVERT: X 1169 MET cc_start: 0.9163 (tpp) cc_final: 0.8667 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.3127
  time to fit residues: 29.8579
Evaluate side-chains
  50 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 1.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 90 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 148 optimal weight:    8.9990
   chunk 68 optimal weight:    4.9990
   chunk 109 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 59 optimal weight:    9.9990
   chunk 43 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 11 optimal weight:   20.0000
   chunk 70 optimal weight:   10.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 342 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.032728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.026507 restraints weight = 385696.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.027100 restraints weight = 253829.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.027442 restraints weight = 187917.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.5695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  22566  Z= 0.194
  Angle     :  0.613  10.745  32133  Z= 0.346
  Chirality :  0.037   0.233   3702
  Planarity :  0.004   0.059   2702
  Dihedral  : 29.423 178.536   6426
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 19.86
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.61 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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:  1.33 (0.21), residues: 1609
  helix:  1.74 (0.16), residues: 999
  sheet: -1.15 (0.59), residues: 78
  loop : -0.38 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP X 464 
 HIS   0.005   0.001   HIS A 113 
 PHE   0.016   0.002   PHE A  78 
 TYR   0.017   0.001   TYR G  39 
 ARG   0.006   0.000   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06070 ( 1192)
  hydrogen bonds       : angle       4.17441 ( 3110)
  covalent geometry    : bond        0.00406 (22566)
  covalent geometry    : angle       0.61298 (32133)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4994.12 seconds
wall clock time: 89 minutes 28.61 seconds (5368.61 seconds total)