Starting phenix.real_space_refine
on Sun Aug 24 15:59:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yny_39431/08_2025/8yny_39431.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yny_39431/08_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_39431/08_2025/8yny_39431.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yny_39431/08_2025/8yny_39431.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yny_39431/08_2025/8yny_39431.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yny_39431/08_2025/8yny_39431.cif"
  }
  resolution = 4.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.76, per 1000 atoms: 0.18
  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: 1.75
  Conformation dependent library (CDL) restraints added in 536.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 2.70
  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: 4.73

  Time building geometry restraints manager: 2.31 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:             0.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     19.130
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.320
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.001   ARG X1210 
 TYR   0.016   0.002   TYR C  57 
 PHE   0.013   0.002   PHE X1313 
 TRP   0.006   0.001   TRP X 464 
 HIS   0.006   0.001   HIS F  75 

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

*********************** 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  : 0.431 
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: 0.1241
  time to fit residues: 19.1219
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  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 194 optimal weight:    9.9990
   chunk 107 optimal weight:    0.0010
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:   20.0000
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   overall best weight:    6.9994

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.034846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.028734 restraints weight = 377226.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.029237 restraints weight = 258169.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.029575 restraints weight = 200249.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.029841 restraints weight = 167791.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.029983 restraints weight = 148317.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  22566  Z= 0.253
  Angle     :  0.695  11.149  32133  Z= 0.393
  Chirality :  0.040   0.222   3702
  Planarity :  0.005   0.052   2702
  Dihedral  : 29.565 171.660   6426
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 22.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.82 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.20), residues: 1609
  helix:  1.20 (0.16), residues: 1021
  sheet: -0.52 (0.50), residues: 90
  loop : -0.74 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  63 
 TYR   0.017   0.002   TYR X1232 
 PHE   0.017   0.002   PHE X1313 
 TRP   0.012   0.002   TRP X 464 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 (22566)
  covalent geometry    : angle       0.69499 (32133)
  hydrogen bonds       : bond        0.08527 ( 1192)
  hydrogen bonds       : angle       4.52985 ( 3110)

*********************** 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
  68 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.749 
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: symmetry clash
REVERT: A   67 PHE cc_start: 0.9169 (t80) cc_final: 0.8743 (t80)
REVERT: A   90 MET cc_start: 0.9444 (mmp) cc_final: 0.9181 (mmm)
REVERT: D  105 LYS cc_start: 0.9567 (pttm) cc_final: 0.9353 (mptt)
REVERT: D  106 HIS cc_start: 0.9579 (m90) cc_final: 0.9345 (m90)
REVERT: H   59 MET cc_start: 0.9748 (mmm) cc_final: 0.9518 (mmm)
REVERT: H   77 LEU cc_start: 0.9735 (tt) cc_final: 0.9526 (pp)
REVERT: H   79 HIS cc_start: 0.9543 (m90) cc_final: 0.9194 (m90)
REVERT: X  383 MET cc_start: 0.9248 (ttm) cc_final: 0.8984 (ttm)
REVERT: X  751 MET cc_start: 0.9095 (ttm) cc_final: 0.8841 (ttp)
REVERT: X 1169 MET cc_start: 0.9624 (ttm) cc_final: 0.9122 (tpp)
  outliers start: 2
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1654
  time to fit residues: 18.3413
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  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 2 optimal weight:   20.0000
   chunk 96 optimal weight:   30.0000
   chunk 108 optimal weight:    0.6980
   chunk 140 optimal weight:    6.9990
   chunk 51 optimal weight:   30.0000
   chunk 30 optimal weight:    7.9990
   chunk 11 optimal weight:   20.0000
   chunk 93 optimal weight:   10.0000
   chunk 138 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 16 optimal weight:    8.9990
   overall best weight:    3.3984

-------------------------------------------------------------------------------
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 723 HIS
** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.035674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.029388 restraints weight = 373190.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.029960 restraints weight = 251072.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.030312 restraints weight = 188502.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.030575 restraints weight = 156877.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.030755 restraints weight = 138026.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  22566  Z= 0.167
  Angle     :  0.607   8.692  32133  Z= 0.345
  Chirality :  0.037   0.200   3702
  Planarity :  0.004   0.062   2702
  Dihedral  : 29.203 168.631   6426
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 17.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.21), residues: 1609
  helix:  1.56 (0.16), residues: 1015
  sheet: -0.74 (0.53), residues: 84
  loop : -0.58 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.000   ARG F  92 
 TYR   0.019   0.002   TYR X 347 
 PHE   0.020   0.002   PHE C  25 
 TRP   0.006   0.001   TRP X 464 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (22566)
  covalent geometry    : angle       0.60718 (32133)
  hydrogen bonds       : bond        0.05111 ( 1192)
  hydrogen bonds       : angle       4.09442 ( 3110)

*********************** 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
  69 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.654 
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: 0.9149 (t80) cc_final: 0.8903 (t80)
REVERT: A   90 MET cc_start: 0.9386 (mmp) cc_final: 0.9153 (mmm)
REVERT: D  106 HIS cc_start: 0.9596 (m90) cc_final: 0.9341 (m90)
REVERT: G   34 LEU cc_start: 0.9667 (mt) cc_final: 0.9324 (pp)
REVERT: H   68 GLU cc_start: 0.9200 (tt0) cc_final: 0.8996 (tm-30)
REVERT: H   77 LEU cc_start: 0.9731 (tt) cc_final: 0.9506 (pp)
REVERT: X  631 MET cc_start: 0.8731 (ptt) cc_final: 0.8460 (ptt)
REVERT: X 1169 MET cc_start: 0.9577 (ttm) cc_final: 0.9052 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.1583
  time to fit residues: 17.6375
Evaluate side-chains
  52 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 139 optimal weight:    9.9990
   chunk 161 optimal weight:    6.9990
   chunk 196 optimal weight:    0.9980
   chunk 190 optimal weight:    3.9990
   chunk 82 optimal weight:   30.0000
   chunk 3 optimal weight:    0.8980
   chunk 113 optimal weight:    0.0970
   chunk 88 optimal weight:   10.0000
   chunk 109 optimal weight:    5.9990
   chunk 122 optimal weight:   40.0000
   overall best weight:    2.3982

-------------------------------------------------------------------------------
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**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X1317 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.035758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.029391 restraints weight = 365111.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.029949 restraints weight = 245300.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.030297 restraints weight = 186545.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.030558 restraints weight = 155969.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.030751 restraints weight = 137877.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  22566  Z= 0.150
  Angle     :  0.577   7.312  32133  Z= 0.328
  Chirality :  0.036   0.208   3702
  Planarity :  0.004   0.056   2702
  Dihedral  : 28.959 176.786   6426
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.05 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.21), residues: 1609
  helix:  1.80 (0.16), residues: 1009
  sheet: -0.70 (0.53), residues: 91
  loop : -0.44 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  92 
 TYR   0.012   0.001   TYR X 430 
 PHE   0.014   0.001   PHE A  78 
 TRP   0.005   0.001   TRP X1074 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (22566)
  covalent geometry    : angle       0.57691 (32133)
  hydrogen bonds       : bond        0.04470 ( 1192)
  hydrogen bonds       : angle       3.86457 ( 3110)

*********************** 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
  69 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.543 
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: 0.9019 (t80) cc_final: 0.8797 (t80)
REVERT: A   90 MET cc_start: 0.9413 (mmp) cc_final: 0.9182 (mmm)
REVERT: A  120 MET cc_start: 0.7670 (mpp) cc_final: 0.7415 (mpp)
REVERT: D  106 HIS cc_start: 0.9552 (m90) cc_final: 0.9214 (m90)
REVERT: G  102 ILE cc_start: 0.7053 (mp) cc_final: 0.6783 (tt)
REVERT: H   68 GLU cc_start: 0.9259 (tt0) cc_final: 0.8973 (tm-30)
REVERT: H   77 LEU cc_start: 0.9675 (tt) cc_final: 0.9409 (pp)
REVERT: X  383 MET cc_start: 0.8647 (ttm) cc_final: 0.8398 (ttt)
REVERT: X  631 MET cc_start: 0.9079 (ptt) cc_final: 0.8842 (ptt)
REVERT: X 1169 MET cc_start: 0.9631 (ttm) cc_final: 0.9066 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.1530
  time to fit residues: 17.2688
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  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 135 optimal weight:    5.9990
   chunk 12 optimal weight:   40.0000
   chunk 53 optimal weight:   30.0000
   chunk 115 optimal weight:    0.4980
   chunk 183 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 172 optimal weight:    9.9990
   chunk 52 optimal weight:   20.0000
   chunk 195 optimal weight:   30.0000
   chunk 28 optimal weight:   10.0000
   overall best weight:    6.6990

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  24 GLN
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X1297 HIS
X1308 ASN
X1317 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.033039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.026873 restraints weight = 391445.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.027439 restraints weight = 257709.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.027779 restraints weight = 191903.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.028046 restraints weight = 159018.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.028220 restraints weight = 138747.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  22566  Z= 0.239
  Angle     :  0.644   7.696  32133  Z= 0.367
  Chirality :  0.038   0.230   3702
  Planarity :  0.005   0.062   2702
  Dihedral  : 29.529 177.052   6426
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 22.80
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.42 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.21), residues: 1609
  helix:  1.57 (0.16), residues: 1012
  sheet: -1.02 (0.53), residues: 91
  loop : -0.43 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG X 324 
 TYR   0.020   0.002   TYR D  34 
 PHE   0.015   0.002   PHE E  67 
 TRP   0.012   0.002   TRP X 464 
 HIS   0.007   0.001   HIS X 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 (22566)
  covalent geometry    : angle       0.64363 (32133)
  hydrogen bonds       : bond        0.07445 ( 1192)
  hydrogen bonds       : angle       4.23631 ( 3110)

*********************** 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
  64 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.742 
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: 0.9200 (t80) cc_final: 0.8773 (t80)
REVERT: A   90 MET cc_start: 0.9424 (mmp) cc_final: 0.9102 (mmp)
REVERT: D  106 HIS cc_start: 0.9660 (m90) cc_final: 0.9406 (m90)
REVERT: E   67 PHE cc_start: 0.9262 (t80) cc_final: 0.9046 (t80)
REVERT: G  102 ILE cc_start: 0.7454 (mp) cc_final: 0.7062 (tt)
REVERT: H   56 MET cc_start: 0.8564 (tpp) cc_final: 0.8332 (tpt)
REVERT: H   59 MET cc_start: 0.9715 (ttm) cc_final: 0.9400 (tmm)
REVERT: H   68 GLU cc_start: 0.9201 (tt0) cc_final: 0.8962 (tm-30)
REVERT: H   77 LEU cc_start: 0.9605 (tt) cc_final: 0.9319 (pp)
REVERT: H   79 HIS cc_start: 0.9470 (m90) cc_final: 0.9158 (m90)
REVERT: X   90 MET cc_start: 0.9450 (tmm) cc_final: 0.9228 (tmm)
REVERT: X  383 MET cc_start: 0.9253 (ttm) cc_final: 0.8844 (ttm)
REVERT: X  631 MET cc_start: 0.8521 (ptt) cc_final: 0.8244 (ptt)
REVERT: X  751 MET cc_start: 0.9058 (ttm) cc_final: 0.8574 (ttm)
REVERT: X 1169 MET cc_start: 0.9554 (ttm) cc_final: 0.9051 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1542
  time to fit residues: 16.4537
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  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 58 optimal weight:    9.9990
   chunk 35 optimal weight:   20.0000
   chunk 92 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 43 optimal weight:    8.9990
   chunk 194 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 193 optimal weight:    7.9990
   chunk 96 optimal weight:   30.0000
   overall best weight:    7.3990

-------------------------------------------------------------------------------
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**
** C  84 GLN ** 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  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X1311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.032369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.026180 restraints weight = 394351.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.026738 restraints weight = 260810.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.027088 restraints weight = 194992.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.027353 restraints weight = 161143.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.027506 restraints weight = 140994.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.4715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  22566  Z= 0.252
  Angle     :  0.668  11.421  32133  Z= 0.378
  Chirality :  0.039   0.219   3702
  Planarity :  0.005   0.059   2702
  Dihedral  : 29.718 179.891   6426
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 24.27
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.80 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.21), residues: 1609
  helix:  1.44 (0.16), residues: 1003
  sheet: -1.19 (0.57), residues: 83
  loop : -0.38 (0.27), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG X 340 
 TYR   0.017   0.002   TYR G  39 
 PHE   0.013   0.002   PHE X 462 
 TRP   0.009   0.002   TRP X 659 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 (22566)
  covalent geometry    : angle       0.66818 (32133)
  hydrogen bonds       : bond        0.07919 ( 1192)
  hydrogen bonds       : angle       4.35089 ( 3110)

*********************** 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  : 0.676 
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: 0.9276 (t80) cc_final: 0.8859 (t80)
REVERT: A   90 MET cc_start: 0.9404 (mmp) cc_final: 0.9039 (mmp)
REVERT: A  120 MET cc_start: 0.7129 (mpp) cc_final: 0.6881 (mpp)
REVERT: D  106 HIS cc_start: 0.9671 (m90) cc_final: 0.9470 (m90)
REVERT: G  102 ILE cc_start: 0.7113 (mp) cc_final: 0.6657 (tt)
REVERT: H   66 ILE cc_start: 0.9280 (pt) cc_final: 0.9079 (pt)
REVERT: H   77 LEU cc_start: 0.9538 (tt) cc_final: 0.9253 (pp)
REVERT: H   79 HIS cc_start: 0.9464 (m90) cc_final: 0.9124 (m90)
REVERT: X  383 MET cc_start: 0.9307 (ttm) cc_final: 0.8823 (ttm)
REVERT: X  631 MET cc_start: 0.7966 (ptt) cc_final: 0.7708 (ptt)
REVERT: X  751 MET cc_start: 0.9115 (ttm) cc_final: 0.8635 (ttm)
REVERT: X 1169 MET cc_start: 0.9558 (ttm) cc_final: 0.9101 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1559
  time to fit residues: 15.1003
Evaluate side-chains
  45 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 109 optimal weight:   30.0000
   chunk 122 optimal weight:   20.0000
   chunk 51 optimal weight:    8.9990
   chunk 80 optimal weight:   20.0000
   chunk 76 optimal weight:   10.0000
   chunk 93 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 193 optimal weight:    6.9990
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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**
C  84 GLN
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  60 ASN
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 926 GLN
** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.032158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.025969 restraints weight = 395657.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.026554 restraints weight = 255970.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.026895 restraints weight = 188651.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.027156 restraints weight = 155757.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.027336 restraints weight = 135729.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.5219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  22566  Z= 0.242
  Angle     :  0.662  11.529  32133  Z= 0.376
  Chirality :  0.039   0.223   3702
  Planarity :  0.005   0.062   2702
  Dihedral  : 29.811 178.050   6426
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 24.37
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.92 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.21), residues: 1609
  helix:  1.33 (0.16), residues: 1004
  sheet: -1.29 (0.56), residues: 83
  loop : -0.40 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG D  76 
 TYR   0.017   0.002   TYR G  39 
 PHE   0.017   0.002   PHE X 688 
 TRP   0.015   0.002   TRP X 464 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (22566)
  covalent geometry    : angle       0.66199 (32133)
  hydrogen bonds       : bond        0.07701 ( 1192)
  hydrogen bonds       : angle       4.36837 ( 3110)

*********************** 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
  55 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9294 (t80) cc_final: 0.8876 (t80)
REVERT: A   90 MET cc_start: 0.9391 (mmp) cc_final: 0.9021 (mmp)
REVERT: A  120 MET cc_start: 0.6362 (mpp) cc_final: 0.5969 (mpp)
REVERT: E   67 PHE cc_start: 0.9223 (t80) cc_final: 0.8975 (t80)
REVERT: G  102 ILE cc_start: 0.7080 (mp) cc_final: 0.6608 (tt)
REVERT: H   56 MET cc_start: 0.8240 (tpt) cc_final: 0.8035 (tpt)
REVERT: H   66 ILE cc_start: 0.9293 (pt) cc_final: 0.9084 (pt)
REVERT: H   77 LEU cc_start: 0.9778 (tt) cc_final: 0.9528 (pp)
REVERT: H   79 HIS cc_start: 0.9471 (m90) cc_final: 0.9117 (m90)
REVERT: X  631 MET cc_start: 0.8104 (ptt) cc_final: 0.7834 (ptt)
REVERT: X  751 MET cc_start: 0.9058 (ttm) cc_final: 0.8606 (ttm)
REVERT: X 1169 MET cc_start: 0.9466 (ttm) cc_final: 0.8919 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1452
  time to fit residues: 13.5250
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  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 106 optimal weight:   20.0000
   chunk 89 optimal weight:   10.0000
   chunk 96 optimal weight:   30.0000
   chunk 70 optimal weight:   10.0000
   chunk 124 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 53 optimal weight:   40.0000
   chunk 121 optimal weight:    3.9990
   chunk 92 optimal weight:   10.0000
   chunk 170 optimal weight:    6.9990
   chunk 71 optimal weight:    8.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  60 ASN
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 412 HIS
** 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 = 0.3078 r_free = 0.3078 target = 0.032768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.026478 restraints weight = 388441.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.027077 restraints weight = 250627.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.027423 restraints weight = 184390.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.027708 restraints weight = 151844.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.027895 restraints weight = 131366.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.5376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  22566  Z= 0.189
  Angle     :  0.624  11.284  32133  Z= 0.353
  Chirality :  0.038   0.216   3702
  Planarity :  0.004   0.060   2702
  Dihedral  : 29.601 179.497   6426
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.80 %
    Favored  : 97.14 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.21), residues: 1609
  helix:  1.51 (0.16), residues: 1006
  sheet: -1.13 (0.63), residues: 68
  loop : -0.41 (0.27), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E  63 
 TYR   0.020   0.002   TYR X 347 
 PHE   0.014   0.002   PHE C  25 
 TRP   0.008   0.002   TRP X 476 
 HIS   0.010   0.001   HIS X 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (22566)
  covalent geometry    : angle       0.62421 (32133)
  hydrogen bonds       : bond        0.05926 ( 1192)
  hydrogen bonds       : angle       4.18754 ( 3110)

*********************** 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
  56 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9256 (t80) cc_final: 0.8836 (t80)
REVERT: A   90 MET cc_start: 0.9399 (mmp) cc_final: 0.9046 (mmm)
REVERT: A  120 MET cc_start: 0.6951 (mpp) cc_final: 0.6731 (mpp)
REVERT: G  102 ILE cc_start: 0.6949 (mp) cc_final: 0.6385 (tt)
REVERT: H   56 MET cc_start: 0.8264 (tpt) cc_final: 0.8042 (tpt)
REVERT: H   66 ILE cc_start: 0.9299 (pt) cc_final: 0.9075 (pt)
REVERT: H   77 LEU cc_start: 0.9770 (tt) cc_final: 0.9526 (pp)
REVERT: H   79 HIS cc_start: 0.9479 (m90) cc_final: 0.9101 (m90)
REVERT: X  631 MET cc_start: 0.8092 (ptt) cc_final: 0.7749 (ptt)
REVERT: X  751 MET cc_start: 0.9307 (ttm) cc_final: 0.8895 (ttm)
REVERT: X 1169 MET cc_start: 0.9555 (ttm) cc_final: 0.9056 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1497
  time to fit residues: 14.3753
Evaluate side-chains
  43 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 144 optimal weight:   40.0000
   chunk 55 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 174 optimal weight:   20.0000
   chunk 79 optimal weight:   10.0000
   chunk 152 optimal weight:   40.0000
   chunk 124 optimal weight:    5.9990
   chunk 156 optimal weight:    0.4980
   chunk 171 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    4.8988

-------------------------------------------------------------------------------
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  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  60 ASN
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.032504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.026307 restraints weight = 390260.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.026894 restraints weight = 256891.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.027227 restraints weight = 190041.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.027489 restraints weight = 157091.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.027668 restraints weight = 137033.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.5605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  22566  Z= 0.200
  Angle     :  0.631  11.044  32133  Z= 0.357
  Chirality :  0.037   0.230   3702
  Planarity :  0.004   0.060   2702
  Dihedral  : 29.658 179.572   6426
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 21.66
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.80 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.21), residues: 1609
  helix:  1.57 (0.16), residues: 1004
  sheet: -1.05 (0.61), residues: 78
  loop : -0.38 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E  63 
 TYR   0.017   0.002   TYR G  39 
 PHE   0.015   0.002   PHE E  67 
 TRP   0.011   0.001   TRP X 464 
 HIS   0.008   0.001   HIS X 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (22566)
  covalent geometry    : angle       0.63053 (32133)
  hydrogen bonds       : bond        0.06480 ( 1192)
  hydrogen bonds       : angle       4.27591 ( 3110)

*********************** 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
  56 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.710 
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: 0.9241 (t80) cc_final: 0.8775 (t80)
REVERT: A   78 PHE cc_start: 0.9376 (t80) cc_final: 0.9119 (t80)
REVERT: A   90 MET cc_start: 0.9393 (mmp) cc_final: 0.9030 (mmp)
REVERT: D   59 MET cc_start: 0.9802 (mmp) cc_final: 0.9594 (mmm)
REVERT: E   67 PHE cc_start: 0.9169 (t80) cc_final: 0.8922 (t80)
REVERT: G  102 ILE cc_start: 0.7055 (mp) cc_final: 0.6555 (tt)
REVERT: H   66 ILE cc_start: 0.9301 (pt) cc_final: 0.9085 (pt)
REVERT: H   77 LEU cc_start: 0.9792 (tt) cc_final: 0.9545 (pp)
REVERT: H   79 HIS cc_start: 0.9476 (m90) cc_final: 0.9096 (m90)
REVERT: X  383 MET cc_start: 0.9139 (ttt) cc_final: 0.8362 (tmm)
REVERT: X  631 MET cc_start: 0.8181 (ptt) cc_final: 0.7832 (ptt)
REVERT: X  751 MET cc_start: 0.9282 (ttm) cc_final: 0.8866 (ttm)
REVERT: X 1169 MET cc_start: 0.9487 (ttm) cc_final: 0.8921 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1443
  time to fit residues: 13.6006
Evaluate side-chains
  45 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 159 optimal weight:    6.9990
   chunk 177 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 59 optimal weight:    9.9990
   chunk 118 optimal weight:    5.9990
   chunk 129 optimal weight:   10.0000
   chunk 180 optimal weight:    5.9990
   chunk 92 optimal weight:   10.0000
   chunk 134 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  60 ASN
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.031971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.025789 restraints weight = 393669.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.026364 restraints weight = 259161.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.026701 restraints weight = 191662.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.026977 restraints weight = 158371.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.027151 restraints weight = 137161.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.5923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  22566  Z= 0.233
  Angle     :  0.659  12.194  32133  Z= 0.372
  Chirality :  0.038   0.247   3702
  Planarity :  0.005   0.061   2702
  Dihedral  : 29.881 178.970   6426
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 23.59
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.98 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.21), residues: 1609
  helix:  1.50 (0.16), residues: 986
  sheet: -1.12 (0.66), residues: 66
  loop : -0.42 (0.27), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  63 
 TYR   0.017   0.002   TYR G  39 
 PHE   0.019   0.002   PHE X 462 
 TRP   0.008   0.002   TRP X1126 
 HIS   0.008   0.001   HIS X 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 (22566)
  covalent geometry    : angle       0.65912 (32133)
  hydrogen bonds       : bond        0.07532 ( 1192)
  hydrogen bonds       : angle       4.38411 ( 3110)

********************** 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
  54 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9270 (t80) cc_final: 0.9014 (t80)
REVERT: A   90 MET cc_start: 0.9386 (mmp) cc_final: 0.9152 (mmp)
REVERT: E   67 PHE cc_start: 0.9179 (t80) cc_final: 0.8857 (t80)
REVERT: G  102 ILE cc_start: 0.7107 (mp) cc_final: 0.6661 (tt)
REVERT: H   66 ILE cc_start: 0.9291 (pt) cc_final: 0.9073 (pt)
REVERT: H   77 LEU cc_start: 0.9781 (tt) cc_final: 0.9527 (pp)
REVERT: H   79 HIS cc_start: 0.9454 (m90) cc_final: 0.9092 (m90)
REVERT: X  383 MET cc_start: 0.9239 (ttt) cc_final: 0.8433 (tmm)
REVERT: X  631 MET cc_start: 0.7990 (ptt) cc_final: 0.7644 (ptt)
REVERT: X  751 MET cc_start: 0.9314 (ttm) cc_final: 0.8917 (ttm)
REVERT: X 1169 MET cc_start: 0.9448 (ttm) cc_final: 0.8905 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1491
  time to fit residues: 13.7868
Evaluate side-chains
  43 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 199
   random chunks:
   chunk 106 optimal weight:   20.0000
   chunk 103 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 113 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 143 optimal weight:    6.9990
   chunk 173 optimal weight:    8.9990
   chunk 185 optimal weight:   20.0000
   chunk 52 optimal weight:    9.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    5.1588

-------------------------------------------------------------------------------
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  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  60 ASN
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 692 ASN
X 983 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.032084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.025949 restraints weight = 389629.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.026516 restraints weight = 257848.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.026851 restraints weight = 192821.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.027111 restraints weight = 159794.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.027306 restraints weight = 139007.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.6085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  22566  Z= 0.199
  Angle     :  0.631  11.779  32133  Z= 0.356
  Chirality :  0.038   0.219   3702
  Planarity :  0.004   0.059   2702
  Dihedral  : 29.768 179.901   6426
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 21.38
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.80 %
    Favored  : 97.14 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.21), residues: 1609
  helix:  1.58 (0.16), residues: 992
  sheet: -1.10 (0.66), residues: 66
  loop : -0.39 (0.27), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E  63 
 TYR   0.017   0.002   TYR G  39 
 PHE   0.017   0.002   PHE A  78 
 TRP   0.027   0.002   TRP X 464 
 HIS   0.006   0.001   HIS X 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (22566)
  covalent geometry    : angle       0.63078 (32133)
  hydrogen bonds       : bond        0.06335 ( 1192)
  hydrogen bonds       : angle       4.26857 ( 3110)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3019.47 seconds
wall clock time: 53 minutes 47.30 seconds (3227.30 seconds total)