Starting phenix.real_space_refine
on Wed Feb  4 17:58:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jwn_61854/02_2026/9jwn_61854.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jwn_61854/02_2026/9jwn_61854.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jwn_61854/02_2026/9jwn_61854.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jwn_61854/02_2026/9jwn_61854.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jwn_61854/02_2026/9jwn_61854.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jwn_61854/02_2026/9jwn_61854.cif"
  }
  resolution = 2.89
  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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 107 atoms to isotropic.
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     152      5.49       5
     S      31      5.16       5
     C    6992      2.51       5
     N    2053      2.21       5
     O    2667      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11895
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "D"
      Number of atoms: 268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 268
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
    Chain: "B"
      Number of atoms: 2380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 2380
          Classifications: {'RNA': 112}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 13, 'rna3p_pur': 52, 'rna3p_pyr': 41}
          Link IDs: {'rna2p': 19, 'rna3p': 92}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 552
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "A"
      Number of atoms: 8691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1063, 8691
          Classifications: {'peptide': 1063}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 1030}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.72, per 1000 atoms: 0.23
  Number of scatterers: 11895
  At special positions: 0
  Unit cell: (114.688, 122.88, 117.965, 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      31     16.00
     P     152     15.00
     O    2667      8.00
     N    2053      7.00
     C    6992      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: 1.10
  Conformation dependent library (CDL) restraints added in 509.3 milliseconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2018

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 6 sheets defined
      49.9% alpha, 7.0% beta
      42 base pairs and 102 stacking pairs defined.
    Time for finding SS restraints: 1.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 84
      removed outlier: 4.559A  pdb=" N   ARG A  60 " --> pdb=" O   THR A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 90
      removed outlier: 3.705A  pdb=" N   LYS A  90 " --> pdb=" O   ASN A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 93
      No H-bonds generated for 'chain 'A' and resid 91 through 93'
    Processing helix  chain 'A' and resid 94 through 101
      removed outlier: 3.695A  pdb=" N   GLU A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 132
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 180 through 190
      removed outlier: 3.753A  pdb=" N   GLN A 186 " --> pdb=" O   GLU A 182 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   PHE A 187 " --> pdb=" O   GLU A 183 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASP A 190 " --> pdb=" O   GLN A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 204
    Processing helix  chain 'A' and resid 204 through 214
    Processing helix  chain 'A' and resid 218 through 231
      removed outlier: 3.560A  pdb=" N   ILE A 226 " --> pdb=" O   LYS A 222 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU A 227 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU A 228 " --> pdb=" O   GLN A 224 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ILE A 229 " --> pdb=" O   GLN A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 287
      Proline residue:  A 284  - end of helix
    Processing helix  chain 'A' and resid 300 through 312
      removed outlier: 3.578A  pdb=" N   LEU A 304 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   TYR A 305 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 352
      removed outlier: 3.573A  pdb=" N   ALA A 332 " --> pdb=" O   GLU A 328 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LYS A 343 " --> pdb=" O   SER A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 360
      removed outlier: 3.584A  pdb=" N   PHE A 359 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 373
    Processing helix  chain 'A' and resid 389 through 402
      removed outlier: 3.560A  pdb=" N   GLU A 402 " --> pdb=" O   ASN A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 420
    Processing helix  chain 'A' and resid 435 through 452
      removed outlier: 3.922A  pdb=" N   GLU A 442 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LYS A 452 " --> pdb=" O   GLN A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 459
      removed outlier: 3.927A  pdb=" N   GLU A 459 " --> pdb=" O   PHE A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 477
    Processing helix  chain 'A' and resid 512 through 517
    Processing helix  chain 'A' and resid 518 through 531
      removed outlier: 3.515A  pdb=" N   ILE A 527 " --> pdb=" O   ALA A 523 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU A 530 " --> pdb=" O   PHE A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 562
      removed outlier: 3.589A  pdb=" N   GLU A 554 " --> pdb=" O   TYR A 550 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL A 555 " --> pdb=" O   GLN A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 636
      removed outlier: 4.788A  pdb=" N   GLU A 633 " --> pdb=" O   LYS A 629 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   LEU A 634 " --> pdb=" O   LYS A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 658
      removed outlier: 3.800A  pdb=" N   ILE A 651 " --> pdb=" O   MET A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 673
      removed outlier: 3.945A  pdb=" N   LEU A 665 " --> pdb=" O   SER A 661 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ARG A 667 " --> pdb=" O   LYS A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 687
    Processing helix  chain 'A' and resid 696 through 701
    Processing helix  chain 'A' and resid 715 through 722
      removed outlier: 3.607A  pdb=" N   LEU A 719 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ARG A 720 " --> pdb=" O   ILE A 716 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   THR A 722 " --> pdb=" O   ALA A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 734 through 744
      removed outlier: 4.326A  pdb=" N   LYS A 738 " --> pdb=" O   SER A 734 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLN A 741 " --> pdb=" O   ALA A 737 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU A 742 " --> pdb=" O   LYS A 738 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   LEU A 743 " --> pdb=" O   LYS A 739 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASN A 744 " --> pdb=" O   LEU A 740 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 784
      removed outlier: 3.710A  pdb=" N   GLU A 781 " --> pdb=" O   LEU A 777 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ASP A 784 " --> pdb=" O   ARG A 780 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 976
      removed outlier: 3.559A  pdb=" N   SER A 971 " --> pdb=" O   LYS A 967 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LEU A 972 " --> pdb=" O   ALA A 968 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   CYS A 976 " --> pdb=" O   LEU A 972 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 988 through 997
    Processing helix  chain 'A' and resid 1007 through 1021
      removed outlier: 4.210A  pdb=" N   ALA A1011 " --> pdb=" O   ASN A1007 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE A1018 " --> pdb=" O   ALA A1014 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL A1019 " --> pdb=" O   TYR A1015 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1072 through 1082
    Processing helix  chain 'A' and resid 1122 through 1127
      removed outlier: 3.538A  pdb=" N   ASN A1127 " --> pdb=" O   SER A1123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1128 through 1133
    Processing helix  chain 'A' and resid 1164 through 1166
      No H-bonds generated for 'chain 'A' and resid 1164 through 1166'
    Processing helix  chain 'A' and resid 1171 through 1182
    Processing helix  chain 'A' and resid 1229 through 1244
      removed outlier: 4.065A  pdb=" N   ALA A1234 " --> pdb=" O   ALA A1230 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   HIS A1235 " --> pdb=" O   LYS A1231 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LYS A1241 " --> pdb=" O   ARG A1237 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE A1242 " --> pdb=" O   MET A1238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1256 through 1274
      removed outlier: 3.605A  pdb=" N   GLU A1272 " --> pdb=" O   ASP A1268 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   HIS A1274 " --> pdb=" O   LEU A1270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1277 through 1281
    Processing helix  chain 'A' and resid 1286 through 1293
    Processing helix  chain 'A' and resid 1293 through 1299
      removed outlier: 3.619A  pdb=" N   VAL A1298 " --> pdb=" O   ARG A1294 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS A1299 " --> pdb=" O   GLU A1295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1301 through 1307
    Processing helix  chain 'A' and resid 1308 through 1314
    Processing helix  chain 'A' and resid 1315 through 1317
      No H-bonds generated for 'chain 'A' and resid 1315 through 1317'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 981 through 984
      removed outlier: 5.912A  pdb=" N   ILE A 793 " --> pdb=" O   VAL A 983 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ILE A  17 " --> pdb=" O   PHE A 794 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1116 through 1117
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1189 through 1195
      removed outlier: 9.843A  pdb=" N   ASP A1189 " --> pdb=" O   GLN A1149 " (cutoff:3.500A)
      removed outlier: 8.764A  pdb=" N   GLN A1149 " --> pdb=" O   ASP A1189 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ARG A1191 " --> pdb=" O   GLU A1147 " (cutoff:3.500A)
      removed outlier: 8.249A  pdb=" N   GLU A1147 " --> pdb=" O   ARG A1191 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   THR A1193 " --> pdb=" O   LEU A1145 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   LEU A1145 " --> pdb=" O   THR A1193 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL A1161 " --> pdb=" O   SER A1141 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   PHE A1143 " --> pdb=" O   GLU A1159 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   GLU A1159 " --> pdb=" O   PHE A1143 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   LEU A1145 " --> pdb=" O   SER A1157 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   SER A1157 " --> pdb=" O   LEU A1145 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   GLU A1147 " --> pdb=" O   ILE A1155 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE A1155 " --> pdb=" O   GLU A1147 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   GLN A1149 " --> pdb=" O   LYS A1153 " (cutoff:3.500A)
      removed outlier: 5.326A  pdb=" N   LYS A1153 " --> pdb=" O   GLN A1149 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ARG A1156 " --> pdb=" O   LEU A1344 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1199 through 1203
      removed outlier: 3.812A  pdb=" N   SER A1199 " --> pdb=" O   LEU A1210 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE A1340 " --> pdb=" O   LEU A1218 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   MET A1338 " --> pdb=" O   LEU A1220 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1355 through 1357

    320 hydrogen bonds defined for protein.
    933 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      96 hydrogen bonds
      180 hydrogen bond angles
      0 basepair planarities
      42 basepair parallelities
      102 stacking parallelities
  Total time for adding SS restraints: 2.66

  Time building geometry restraints manager: 1.40 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: 2744
        1.33 -     1.45: 3289
        1.45 -     1.57: 6047
        1.57 -     1.69: 300
        1.69 -     1.81: 51
  Bond restraints: 12431
  Sorted by residual:
  bond pdb=" C   ARG A 139 "
       pdb=" O   ARG A 139 "
    ideal  model  delta    sigma   weight residual
    1.237  1.219  0.018 1.17e-02 7.31e+03 2.41e+00
  bond pdb=" N   ASP A1136 "
       pdb=" CA  ASP A1136 "
    ideal  model  delta    sigma   weight residual
    1.453  1.470 -0.018 1.31e-02 5.83e+03 1.83e+00
  bond pdb=" C3'  DA C  -6 "
       pdb=" O3'  DA C  -6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.463 -0.041 3.00e-02 1.11e+03 1.83e+00
  bond pdb=" C3'  DG D  -2 "
       pdb=" O3'  DG D  -2 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.45e+00
  bond pdb=" C   LEU A 138 "
       pdb=" O   LEU A 138 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.013 1.15e-02 7.56e+03 1.30e+00
  ... (remaining 12426 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 17196
        1.95 -     3.91: 235
        3.91 -     5.86: 28
        5.86 -     7.81: 3
        7.81 -     9.76: 2
  Bond angle restraints: 17464
  Sorted by residual:
  angle pdb=" C3'   U B 101 "
        pdb=" O3'   U B 101 "
        pdb=" P     G B 102 "
      ideal   model   delta    sigma   weight residual
     120.20  125.63   -5.43 1.50e+00 4.44e-01 1.31e+01
  angle pdb=" N   HIS A 137 "
        pdb=" CA  HIS A 137 "
        pdb=" C   HIS A 137 "
      ideal   model   delta    sigma   weight residual
     111.36  107.88    3.48 1.09e+00 8.42e-01 1.02e+01
  angle pdb=" N   ASN A 732 "
        pdb=" CA  ASN A 732 "
        pdb=" C   ASN A 732 "
      ideal   model   delta    sigma   weight residual
     111.71  115.32   -3.61 1.15e+00 7.56e-01 9.87e+00
  angle pdb=" C4'   U B 101 "
        pdb=" C3'   U B 101 "
        pdb=" O3'   U B 101 "
      ideal   model   delta    sigma   weight residual
     109.40  113.81   -4.41 1.50e+00 4.44e-01 8.65e+00
  angle pdb=" CA  LEU A 257 "
        pdb=" CB  LEU A 257 "
        pdb=" CG  LEU A 257 "
      ideal   model   delta    sigma   weight residual
     116.30  126.06   -9.76 3.50e+00 8.16e-02 7.78e+00
  ... (remaining 17459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 6913
       35.97 -    71.94: 574
       71.94 -   107.92: 47
      107.92 -   143.89: 3
      143.89 -   179.86: 7
  Dihedral angle restraints: 7544
    sinusoidal: 4416
      harmonic: 3128
  Sorted by residual:
  dihedral pdb=" O4'   C B  69 "
           pdb=" C1'   C B  69 "
           pdb=" N1    C B  69 "
           pdb=" C2    C B  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   45.24  154.76     1      1.50e+01 4.44e-03 8.13e+01
  dihedral pdb=" O4'   U B  85 "
           pdb=" C1'   U B  85 "
           pdb=" N1    U B  85 "
           pdb=" C2    U B  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   52.14  179.86     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U B  93 "
           pdb=" C1'   U B  93 "
           pdb=" N1    U B  93 "
           pdb=" C2    U B  93 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   55.34  176.66     1      1.70e+01 3.46e-03 6.64e+01
  ... (remaining 7541 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1752
       0.049 -    0.098: 237
       0.098 -    0.147: 31
       0.147 -    0.197: 1
       0.197 -    0.246: 1
  Chirality restraints: 2022
  Sorted by residual:
  chirality pdb=" C3'   U B 101 "
            pdb=" C4'   U B 101 "
            pdb=" O3'   U B 101 "
            pdb=" C2'   U B 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.50   -0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CB  ILE A 298 "
            pdb=" CA  ILE A 298 "
            pdb=" CG1 ILE A 298 "
            pdb=" CG2 ILE A 298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.70e-01
  chirality pdb=" P    DG C  15 "
            pdb=" OP1  DG C  15 "
            pdb=" OP2  DG C  15 "
            pdb=" O5'  DG C  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.49   -0.14 2.00e-01 2.50e+01 5.18e-01
  ... (remaining 2019 not shown)

  Planarity restraints: 1674
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A1287 "   -0.042 5.00e-02 4.00e+02   6.42e-02 6.59e+00
        pdb=" N   PRO A1288 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A1288 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A1288 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 977 "    0.038 5.00e-02 4.00e+02   5.78e-02 5.35e+00
        pdb=" N   PRO A 978 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 978 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 978 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 766 "    0.030 5.00e-02 4.00e+02   4.49e-02 3.22e+00
        pdb=" N   PRO A 767 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 767 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 767 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1671 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1119
        2.74 -     3.28: 11598
        3.28 -     3.82: 21688
        3.82 -     4.36: 27519
        4.36 -     4.90: 41182
  Nonbonded interactions: 103106
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 394 "
            pdb=" O   PHE A 422 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   THR A1076 "
            pdb=" OG1 THR A1080 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   SER A 520 "
            pdb=" OH  TYR A 658 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OG1 THR A 535 "
            pdb=" O   ASN A 694 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O2'   U B  62 "
            pdb=" OE1 GLN A 426 "
     model   vdw
     2.231 3.040
  ... (remaining 103101 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.670
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12431  Z= 0.146
  Angle     :  0.543   9.763  17464  Z= 0.292
  Chirality :  0.034   0.246   2022
  Planarity :  0.004   0.064   1674
  Dihedral  : 22.601 179.862   5526
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 32.60 %
    Favored  : 64.99 %
  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 are not related in a simple way.
  whole: -1.12 (0.25), residues: 1047
  helix: -0.30 (0.24), residues: 455
  sheet: -0.50 (0.85), residues: 50
  loop : -1.09 (0.26), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A1003 
 TYR   0.011   0.001   TYR A 322 
 PHE   0.030   0.001   PHE A 553 
 TRP   0.005   0.001   TRP A 496 
 HIS   0.008   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (12431)
  covalent geometry    : angle       0.54278 (17464)
  hydrogen bonds       : bond        0.26673 (  416)
  hydrogen bonds       : angle       8.43096 ( 1113)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A   12 ASN cc_start: 0.5425 (m-40) cc_final: 0.4954 (m110)
REVERT: A   32 ASP cc_start: 0.7119 (p0) cc_final: 0.6763 (p0)
REVERT: A   34 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7444 (mp0)
REVERT: A   78 ARG cc_start: 0.7696 (ttp80) cc_final: 0.7350 (ttp80)
REVERT: A   85 GLN cc_start: 0.7023 (tt0) cc_final: 0.6674 (tt0)
REVERT: A  105 VAL cc_start: 0.8124 (t) cc_final: 0.7750 (m)
REVERT: A  147 GLU cc_start: 0.6727 (pt0) cc_final: 0.6507 (mm-30)
REVERT: A  192 MET cc_start: 0.3834 (mpt) cc_final: 0.3438 (mpt)
REVERT: A  310 LEU cc_start: 0.7700 (mp) cc_final: 0.7214 (mm)
REVERT: A  313 TYR cc_start: 0.5715 (m-80) cc_final: 0.5497 (m-80)
REVERT: A  315 LYS cc_start: 0.7909 (tptp) cc_final: 0.7576 (tptt)
REVERT: A  362 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7295 (ttmm)
REVERT: A  365 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7129 (tptm)
REVERT: A  453 HIS cc_start: 0.7313 (m-70) cc_final: 0.6845 (m90)
REVERT: A  514 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6764 (mm-30)
REVERT: A  545 LYS cc_start: 0.5451 (tttt) cc_final: 0.5216 (mtpp)
REVERT: A  647 MET cc_start: 0.4179 (tpt) cc_final: 0.2749 (tpt)
REVERT: A  741 GLN cc_start: 0.5861 (OUTLIER) cc_final: 0.5585 (mt0)
REVERT: A  762 MET cc_start: 0.7404 (mtp) cc_final: 0.7134 (mtp)
REVERT: A  789 SER cc_start: 0.8165 (m) cc_final: 0.7841 (p)
REVERT: A  795 MET cc_start: 0.7706 (ptm) cc_final: 0.7228 (ptp)
REVERT: A  797 MET cc_start: 0.5945 (mpt) cc_final: 0.5723 (mmt)
REVERT: A  986 LYS cc_start: 0.6521 (mtpp) cc_final: 0.6160 (mtpt)
REVERT: A 1003 ARG cc_start: 0.7306 (ttm110) cc_final: 0.6297 (ttt90)
REVERT: A 1075 LYS cc_start: 0.7615 (mmtp) cc_final: 0.7040 (mtmp)
REVERT: A 1151 LYS cc_start: 0.7919 (mmtp) cc_final: 0.7705 (mmtp)
REVERT: A 1153 LYS cc_start: 0.7688 (mtmt) cc_final: 0.7462 (mttp)
REVERT: A 1275 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7262 (ttp80)
REVERT: A 1299 LYS cc_start: 0.7639 (mtmt) cc_final: 0.7306 (mtpm)
  outliers start: 23
  outliers final: 15
  residues processed: 114
  average time/residue: 0.6821
  time to fit residues: 83.4052
Evaluate side-chains
  88 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  140 LYS
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  621 PHE
Chi-restraints excluded: chain A residue  741 GLN
Chi-restraints excluded: chain A residue  990 THR
Chi-restraints excluded: chain A residue  991 SER
Chi-restraints excluded: chain A residue 1080 THR
Chi-restraints excluded: chain A residue 1224 VAL
Chi-restraints excluded: chain A residue 1248 THR
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1301 THR
Chi-restraints excluded: chain A residue 1357 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0060
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:   30.0000
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    0.8398

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

Flipped N/Q/H residues before XYZ refinement:
A 532 ASN
A1137 ASN
A1357 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.168797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.134690 restraints weight = 14311.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.10
r_work: 0.3205 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12431  Z= 0.140
  Angle     :  0.597   7.579  17464  Z= 0.313
  Chirality :  0.037   0.249   2022
  Planarity :  0.004   0.059   1674
  Dihedral  : 22.231 179.830   3341
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 27.06 %
    Favored  : 67.40 %
  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 are not related in a simple way.
  whole: -0.79 (0.25), residues: 1047
  helix:  0.14 (0.23), residues: 479
  sheet:  0.07 (1.00), residues: 40
  loop : -1.16 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1003 
 TYR   0.015   0.001   TYR A 550 
 PHE   0.023   0.001   PHE A  63 
 TRP   0.006   0.001   TRP A 307 
 HIS   0.008   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12431)
  covalent geometry    : angle       0.59703 (17464)
  hydrogen bonds       : bond        0.05907 (  416)
  hydrogen bonds       : angle       5.10462 ( 1113)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 82
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.6051 (m-40) cc_final: 0.5582 (m110)
REVERT: A   78 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7844 (ttp80)
REVERT: A   85 GLN cc_start: 0.7678 (tt0) cc_final: 0.7301 (tp-100)
REVERT: A  105 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8386 (m)
REVERT: A  192 MET cc_start: 0.4491 (mpt) cc_final: 0.3964 (mpt)
REVERT: A  313 TYR cc_start: 0.5969 (m-80) cc_final: 0.5750 (m-80)
REVERT: A  365 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7783 (tptm)
REVERT: A  453 HIS cc_start: 0.7730 (m-70) cc_final: 0.7507 (m90)
REVERT: A  675 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.5540 (pp20)
REVERT: A  689 PHE cc_start: 0.6021 (OUTLIER) cc_final: 0.5148 (p90)
REVERT: A  741 GLN cc_start: 0.6552 (OUTLIER) cc_final: 0.5920 (mt0)
REVERT: A  797 MET cc_start: 0.6581 (OUTLIER) cc_final: 0.6120 (mmt)
REVERT: A  972 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6749 (pt)
REVERT: A  996 ARG cc_start: 0.7078 (ptm-80) cc_final: 0.6874 (ptm-80)
REVERT: A 1003 ARG cc_start: 0.7488 (ttm110) cc_final: 0.7114 (ttt90)
REVERT: A 1071 ASP cc_start: 0.4692 (OUTLIER) cc_final: 0.4464 (m-30)
REVERT: A 1151 LYS cc_start: 0.7794 (mmtp) cc_final: 0.7483 (mmtp)
REVERT: A 1166 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8101 (ttpt)
REVERT: A 1237 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.5798 (ttt90)
REVERT: A 1275 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7545 (ttp80)
REVERT: A 1372 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6265 (tp)
  outliers start: 53
  outliers final: 9
  residues processed: 122
  average time/residue: 0.6358
  time to fit residues: 83.2745
Evaluate side-chains
  89 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  626 SER
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  741 GLN
Chi-restraints excluded: chain A residue  797 MET
Chi-restraints excluded: chain A residue  972 LEU
Chi-restraints excluded: chain A residue 1071 ASP
Chi-restraints excluded: chain A residue 1166 LYS
Chi-restraints excluded: chain A residue 1237 ARG
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1301 THR
Chi-restraints excluded: chain A residue 1372 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0970
   chunk 31 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 38 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 87 optimal weight:    0.7980
   chunk 113 optimal weight:    0.3980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A  73 GLN
** A1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1319 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.170571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.139117 restraints weight = 14420.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 1.70
r_work: 0.3293 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12431  Z= 0.129
  Angle     :  0.577  11.475  17464  Z= 0.299
  Chirality :  0.036   0.255   2022
  Planarity :  0.004   0.057   1674
  Dihedral  : 22.121 179.266   3325
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 27.06 %
    Favored  : 68.34 %
  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 are not related in a simple way.
  whole: -0.46 (0.26), residues: 1047
  helix:  0.60 (0.24), residues: 477
  sheet: -0.94 (0.77), residues: 54
  loop : -1.08 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 361 
 TYR   0.015   0.001   TYR A 356 
 PHE   0.016   0.001   PHE A  63 
 TRP   0.009   0.001   TRP A 307 
 HIS   0.007   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12431)
  covalent geometry    : angle       0.57728 (17464)
  hydrogen bonds       : bond        0.05004 (  416)
  hydrogen bonds       : angle       4.63528 ( 1113)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 76
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.6193 (m-40) cc_final: 0.5660 (m110)
REVERT: A   32 ASP cc_start: 0.7317 (p0) cc_final: 0.7034 (t0)
REVERT: A   78 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7637 (ttp80)
REVERT: A   85 GLN cc_start: 0.7563 (tt0) cc_final: 0.7348 (tp-100)
REVERT: A  105 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8334 (m)
REVERT: A  192 MET cc_start: 0.4230 (mpt) cc_final: 0.3745 (mpt)
REVERT: A  214 ASP cc_start: 0.5113 (OUTLIER) cc_final: 0.4907 (t70)
REVERT: A  349 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7538 (ttm-80)
REVERT: A  387 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7843 (mtpt)
REVERT: A  647 MET cc_start: 0.5025 (tpt) cc_final: 0.3731 (tpt)
REVERT: A  675 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.5469 (pp20)
REVERT: A  689 PHE cc_start: 0.6039 (OUTLIER) cc_final: 0.5057 (p90)
REVERT: A  741 GLN cc_start: 0.6406 (OUTLIER) cc_final: 0.5859 (mt0)
REVERT: A  797 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.6067 (mmt)
REVERT: A  996 ARG cc_start: 0.7014 (ptm-80) cc_final: 0.6737 (ptm-80)
REVERT: A 1003 ARG cc_start: 0.7376 (ttm110) cc_final: 0.7076 (ttt90)
REVERT: A 1151 LYS cc_start: 0.7756 (mmtp) cc_final: 0.7493 (mmtp)
REVERT: A 1166 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7946 (ttpt)
REVERT: A 1237 ARG cc_start: 0.6402 (OUTLIER) cc_final: 0.5753 (ttt180)
REVERT: A 1275 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7498 (ttp80)
REVERT: A 1372 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6231 (tp)
  outliers start: 44
  outliers final: 10
  residues processed: 111
  average time/residue: 0.6603
  time to fit residues: 78.7529
Evaluate side-chains
  87 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  387 LYS
Chi-restraints excluded: chain A residue  621 PHE
Chi-restraints excluded: chain A residue  626 SER
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  741 GLN
Chi-restraints excluded: chain A residue  797 MET
Chi-restraints excluded: chain A residue 1004 ASP
Chi-restraints excluded: chain A residue 1087 MET
Chi-restraints excluded: chain A residue 1166 LYS
Chi-restraints excluded: chain A residue 1237 ARG
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1372 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 1 optimal weight:   20.0000
   chunk 70 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 95 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 117 optimal weight:    0.0010
   chunk 91 optimal weight:    0.9990
   overall best weight:    1.7792

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 453 HIS
A1164 HIS
A1263 ASN
A1305 GLN
A1319 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.167503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.135577 restraints weight = 14297.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 1.76
r_work: 0.3232 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12431  Z= 0.181
  Angle     :  0.615   8.366  17464  Z= 0.319
  Chirality :  0.038   0.253   2022
  Planarity :  0.004   0.055   1674
  Dihedral  : 22.207 179.573   3319
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 26.54 %
    Favored  : 68.55 %
  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 are not related in a simple way.
  whole: -0.52 (0.25), residues: 1047
  helix:  0.47 (0.24), residues: 481
  sheet: -0.59 (0.87), residues: 44
  loop : -1.07 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 361 
 TYR   0.015   0.002   TYR A 550 
 PHE   0.020   0.002   PHE A 687 
 TRP   0.013   0.001   TRP A 307 
 HIS   0.005   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (12431)
  covalent geometry    : angle       0.61458 (17464)
  hydrogen bonds       : bond        0.05113 (  416)
  hydrogen bonds       : angle       4.65211 ( 1113)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 71
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.6373 (m-40) cc_final: 0.5884 (m110)
REVERT: A   32 ASP cc_start: 0.7224 (p0) cc_final: 0.7013 (p0)
REVERT: A   78 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7728 (ttp80)
REVERT: A   85 GLN cc_start: 0.7648 (tt0) cc_final: 0.7363 (tp-100)
REVERT: A  105 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8489 (m)
REVERT: A  192 MET cc_start: 0.4273 (mpt) cc_final: 0.3809 (mpt)
REVERT: A  310 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7829 (mm)
REVERT: A  399 LYS cc_start: 0.7056 (mmtp) cc_final: 0.6854 (mttm)
REVERT: A  465 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7568 (mtm)
REVERT: A  647 MET cc_start: 0.5082 (tpt) cc_final: 0.4669 (tpt)
REVERT: A  653 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6534 (tp30)
REVERT: A  675 GLU cc_start: 0.5831 (OUTLIER) cc_final: 0.5443 (pp20)
REVERT: A  689 PHE cc_start: 0.6117 (OUTLIER) cc_final: 0.5038 (p90)
REVERT: A  741 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.5860 (mt0)
REVERT: A  992 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6687 (m-30)
REVERT: A  996 ARG cc_start: 0.7118 (ptm-80) cc_final: 0.6828 (ptm-80)
REVERT: A 1003 ARG cc_start: 0.7486 (ttm110) cc_final: 0.7125 (ttt90)
REVERT: A 1166 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8014 (ttpt)
REVERT: A 1237 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.5860 (ttt180)
REVERT: A 1275 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7711 (ttp80)
REVERT: A 1372 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6328 (tp)
  outliers start: 47
  outliers final: 18
  residues processed: 109
  average time/residue: 0.6992
  time to fit residues: 81.9591
Evaluate side-chains
  94 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 65
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  621 PHE
Chi-restraints excluded: chain A residue  626 SER
Chi-restraints excluded: chain A residue  653 GLU
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  741 GLN
Chi-restraints excluded: chain A residue  992 ASP
Chi-restraints excluded: chain A residue 1004 ASP
Chi-restraints excluded: chain A residue 1087 MET
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1166 LYS
Chi-restraints excluded: chain A residue 1237 ARG
Chi-restraints excluded: chain A residue 1265 ARG
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1298 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1372 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 6 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 68 optimal weight:    8.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.168750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.139089 restraints weight = 14390.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 1.59
r_work: 0.3272 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12431  Z= 0.147
  Angle     :  0.586  12.534  17464  Z= 0.303
  Chirality :  0.037   0.255   2022
  Planarity :  0.004   0.055   1674
  Dihedral  : 22.197 179.064   3319
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 27.59 %
    Favored  : 68.34 %
  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 are not related in a simple way.
  whole: -0.33 (0.26), residues: 1047
  helix:  0.68 (0.24), residues: 475
  sheet: -0.46 (0.86), residues: 44
  loop : -1.02 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 994 
 TYR   0.013   0.001   TYR A 788 
 PHE   0.017   0.001   PHE A 687 
 TRP   0.016   0.001   TRP A 307 
 HIS   0.005   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (12431)
  covalent geometry    : angle       0.58578 (17464)
  hydrogen bonds       : bond        0.04746 (  416)
  hydrogen bonds       : angle       4.48197 ( 1113)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 72
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.6212 (m-40) cc_final: 0.5704 (m110)
REVERT: A   78 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7710 (ttp80)
REVERT: A   85 GLN cc_start: 0.7611 (tt0) cc_final: 0.7357 (tp-100)
REVERT: A  105 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8430 (m)
REVERT: A  192 MET cc_start: 0.4187 (mpt) cc_final: 0.3754 (mpt)
REVERT: A  465 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7509 (mtm)
REVERT: A  647 MET cc_start: 0.4929 (tpt) cc_final: 0.4720 (tpt)
REVERT: A  675 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.5444 (pp20)
REVERT: A  689 PHE cc_start: 0.6029 (OUTLIER) cc_final: 0.5032 (p90)
REVERT: A  741 GLN cc_start: 0.6323 (OUTLIER) cc_final: 0.5963 (mt0)
REVERT: A  797 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.6130 (mmt)
REVERT: A  996 ARG cc_start: 0.7094 (ptm-80) cc_final: 0.6801 (ptm-80)
REVERT: A 1003 ARG cc_start: 0.7388 (ttm110) cc_final: 0.7065 (ttt90)
REVERT: A 1237 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.5831 (ttt180)
REVERT: A 1275 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7708 (ttp80)
REVERT: A 1372 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6222 (tp)
  outliers start: 39
  outliers final: 17
  residues processed: 101
  average time/residue: 0.6682
  time to fit residues: 72.7303
Evaluate side-chains
  91 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 66
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  621 PHE
Chi-restraints excluded: chain A residue  626 SER
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  741 GLN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  771 MET
Chi-restraints excluded: chain A residue  797 MET
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain A residue 1004 ASP
Chi-restraints excluded: chain A residue 1087 MET
Chi-restraints excluded: chain A residue 1214 THR
Chi-restraints excluded: chain A residue 1237 ARG
Chi-restraints excluded: chain A residue 1239 ILE
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1298 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1372 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 69 optimal weight:    8.9990
   chunk 84 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 64 optimal weight:    0.0070
   chunk 15 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   overall best weight:    1.8004

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 975 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.167273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.135777 restraints weight = 14355.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.74
r_work: 0.3230 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12431  Z= 0.180
  Angle     :  0.619  12.977  17464  Z= 0.319
  Chirality :  0.038   0.256   2022
  Planarity :  0.004   0.054   1674
  Dihedral  : 22.242 179.461   3319
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 26.85 %
    Favored  : 68.13 %
  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 are not related in a simple way.
  whole: -0.38 (0.26), residues: 1047
  helix:  0.61 (0.24), residues: 476
  sheet: -0.47 (0.85), residues: 44
  loop : -1.01 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 361 
 TYR   0.017   0.002   TYR A 788 
 PHE   0.020   0.002   PHE A 687 
 TRP   0.020   0.002   TRP A 307 
 HIS   0.005   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (12431)
  covalent geometry    : angle       0.61927 (17464)
  hydrogen bonds       : bond        0.04928 (  416)
  hydrogen bonds       : angle       4.51972 ( 1113)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 72
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.6167 (m-40) cc_final: 0.5684 (m110)
REVERT: A   32 ASP cc_start: 0.7364 (p0) cc_final: 0.7091 (t0)
REVERT: A   78 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7742 (ttp80)
REVERT: A   85 GLN cc_start: 0.7673 (tt0) cc_final: 0.7341 (tp-100)
REVERT: A  105 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8496 (m)
REVERT: A  192 MET cc_start: 0.4205 (mpt) cc_final: 0.3765 (mpt)
REVERT: A  465 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7616 (mtm)
REVERT: A  545 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.7070 (mtpp)
REVERT: A  653 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6607 (tp30)
REVERT: A  675 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5485 (pp20)
REVERT: A  689 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.5119 (p90)
REVERT: A  741 GLN cc_start: 0.6060 (OUTLIER) cc_final: 0.5699 (mt0)
REVERT: A  796 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7073 (tm-30)
REVERT: A  992 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6712 (m-30)
REVERT: A  996 ARG cc_start: 0.7086 (ptm-80) cc_final: 0.6807 (ptm-80)
REVERT: A 1003 ARG cc_start: 0.7431 (ttm110) cc_final: 0.7123 (ttt90)
REVERT: A 1232 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6526 (mp0)
REVERT: A 1237 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.5862 (ttt180)
REVERT: A 1275 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7835 (ttp80)
REVERT: A 1372 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6314 (tp)
  outliers start: 48
  outliers final: 20
  residues processed: 108
  average time/residue: 0.6041
  time to fit residues: 70.7309
Evaluate side-chains
  97 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 66
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  621 PHE
Chi-restraints excluded: chain A residue  626 SER
Chi-restraints excluded: chain A residue  653 GLU
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  741 GLN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  771 MET
Chi-restraints excluded: chain A residue  992 ASP
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1214 THR
Chi-restraints excluded: chain A residue 1232 GLU
Chi-restraints excluded: chain A residue 1237 ARG
Chi-restraints excluded: chain A residue 1239 ILE
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1298 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1372 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 109 optimal weight:    0.8980
   chunk 73 optimal weight:    8.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 975 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.167605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.137756 restraints weight = 14306.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 1.58
r_work: 0.3255 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12431  Z= 0.173
  Angle     :  0.616  13.427  17464  Z= 0.317
  Chirality :  0.038   0.258   2022
  Planarity :  0.004   0.055   1674
  Dihedral  : 22.250 179.424   3319
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 27.69 %
    Favored  : 68.23 %
  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 are not related in a simple way.
  whole: -0.34 (0.26), residues: 1047
  helix:  0.67 (0.24), residues: 476
  sheet: -0.19 (0.86), residues: 42
  loop : -1.06 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1282 
 TYR   0.015   0.002   TYR A 788 
 PHE   0.020   0.002   PHE A 687 
 TRP   0.027   0.002   TRP A 307 
 HIS   0.005   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (12431)
  covalent geometry    : angle       0.61602 (17464)
  hydrogen bonds       : bond        0.04827 (  416)
  hydrogen bonds       : angle       4.45972 ( 1113)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 70
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.6175 (m-40) cc_final: 0.5717 (m110)
REVERT: A   85 GLN cc_start: 0.7654 (tt0) cc_final: 0.7367 (tp-100)
REVERT: A  105 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8491 (m)
REVERT: A  192 MET cc_start: 0.4256 (mpt) cc_final: 0.3830 (mpt)
REVERT: A  653 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6590 (tp30)
REVERT: A  675 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.5517 (pp20)
REVERT: A  689 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.5166 (p90)
REVERT: A  741 GLN cc_start: 0.6141 (OUTLIER) cc_final: 0.5807 (mt0)
REVERT: A  992 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6704 (m-30)
REVERT: A  996 ARG cc_start: 0.7044 (ptm-80) cc_final: 0.6743 (ptm-80)
REVERT: A 1003 ARG cc_start: 0.7388 (ttm110) cc_final: 0.7136 (ttt90)
REVERT: A 1237 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.5878 (ttt180)
REVERT: A 1372 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6280 (tp)
  outliers start: 39
  outliers final: 21
  residues processed: 101
  average time/residue: 0.5792
  time to fit residues: 63.5035
Evaluate side-chains
  95 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 66
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  621 PHE
Chi-restraints excluded: chain A residue  626 SER
Chi-restraints excluded: chain A residue  653 GLU
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  741 GLN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  771 MET
Chi-restraints excluded: chain A residue  992 ASP
Chi-restraints excluded: chain A residue 1004 ASP
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1214 THR
Chi-restraints excluded: chain A residue 1237 ARG
Chi-restraints excluded: chain A residue 1239 ILE
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1298 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1372 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 29 optimal weight:    0.3980
   chunk 96 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0980
   chunk 76 optimal weight:    8.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 975 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.169093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.138179 restraints weight = 14329.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 1.70
r_work: 0.3270 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12431  Z= 0.137
  Angle     :  0.589  13.270  17464  Z= 0.303
  Chirality :  0.037   0.264   2022
  Planarity :  0.004   0.055   1674
  Dihedral  : 22.187 179.183   3319
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 28.53 %
    Favored  : 68.03 %
  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 are not related in a simple way.
  whole: -0.19 (0.26), residues: 1047
  helix:  0.81 (0.24), residues: 476
  sheet: -0.37 (0.84), residues: 44
  loop : -0.97 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 994 
 TYR   0.014   0.001   TYR A 788 
 PHE   0.019   0.001   PHE A 687 
 TRP   0.030   0.001   TRP A 307 
 HIS   0.005   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (12431)
  covalent geometry    : angle       0.58865 (17464)
  hydrogen bonds       : bond        0.04573 (  416)
  hydrogen bonds       : angle       4.33301 ( 1113)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 70
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.6209 (m-40) cc_final: 0.5782 (m110)
REVERT: A   32 ASP cc_start: 0.7250 (p0) cc_final: 0.7020 (t0)
REVERT: A   85 GLN cc_start: 0.7636 (tt0) cc_final: 0.7341 (tp-100)
REVERT: A  105 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8424 (m)
REVERT: A  192 MET cc_start: 0.4237 (mpt) cc_final: 0.3777 (mpt)
REVERT: A  297 TYR cc_start: 0.6254 (m-80) cc_final: 0.5861 (t80)
REVERT: A  465 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7462 (mtm)
REVERT: A  653 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6548 (tp30)
REVERT: A  675 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5462 (pp20)
REVERT: A  689 PHE cc_start: 0.6172 (OUTLIER) cc_final: 0.5035 (p90)
REVERT: A  741 GLN cc_start: 0.6072 (OUTLIER) cc_final: 0.5792 (mt0)
REVERT: A  992 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6694 (m-30)
REVERT: A  996 ARG cc_start: 0.7053 (ptm-80) cc_final: 0.6746 (ptm-80)
REVERT: A 1003 ARG cc_start: 0.7348 (ttm110) cc_final: 0.7085 (ttt90)
REVERT: A 1237 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.5838 (ttt90)
REVERT: A 1372 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6260 (tp)
  outliers start: 33
  outliers final: 22
  residues processed: 95
  average time/residue: 0.5835
  time to fit residues: 60.2725
Evaluate side-chains
  97 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 66
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  621 PHE
Chi-restraints excluded: chain A residue  626 SER
Chi-restraints excluded: chain A residue  653 GLU
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  741 GLN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  771 MET
Chi-restraints excluded: chain A residue  975 GLN
Chi-restraints excluded: chain A residue  992 ASP
Chi-restraints excluded: chain A residue 1004 ASP
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1214 THR
Chi-restraints excluded: chain A residue 1237 ARG
Chi-restraints excluded: chain A residue 1239 ILE
Chi-restraints excluded: chain A residue 1248 THR
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1298 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1372 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 73 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 85 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 119 optimal weight:    3.9990
   chunk 37 optimal weight:   10.0000
   chunk 63 optimal weight:    4.9990
   chunk 32 optimal weight:   20.0000
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 975 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.166419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.135017 restraints weight = 14186.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 1.78
r_work: 0.3201 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12431  Z= 0.214
  Angle     :  0.652  12.419  17464  Z= 0.335
  Chirality :  0.039   0.261   2022
  Planarity :  0.004   0.055   1674
  Dihedral  : 22.244 179.515   3319
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 27.38 %
    Favored  : 68.44 %
  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 are not related in a simple way.
  whole: -0.45 (0.25), residues: 1047
  helix:  0.57 (0.24), residues: 472
  sheet: -0.22 (0.86), residues: 42
  loop : -1.10 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1294 
 TYR   0.018   0.002   TYR A 788 
 PHE   0.021   0.002   PHE A 687 
 TRP   0.036   0.002   TRP A 307 
 HIS   0.005   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (12431)
  covalent geometry    : angle       0.65191 (17464)
  hydrogen bonds       : bond        0.05117 (  416)
  hydrogen bonds       : angle       4.50784 ( 1113)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 65
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.6089 (m-40) cc_final: 0.5612 (m110)
REVERT: A   85 GLN cc_start: 0.7740 (tt0) cc_final: 0.7400 (tp-100)
REVERT: A  105 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8533 (m)
REVERT: A  192 MET cc_start: 0.4209 (mpt) cc_final: 0.3742 (mpt)
REVERT: A  465 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7536 (mtm)
REVERT: A  545 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.7003 (mtpp)
REVERT: A  653 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6681 (tp30)
REVERT: A  675 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.5430 (pp20)
REVERT: A  689 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.4940 (p90)
REVERT: A  741 GLN cc_start: 0.5810 (OUTLIER) cc_final: 0.5554 (mt0)
REVERT: A  992 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6706 (m-30)
REVERT: A  996 ARG cc_start: 0.7115 (ptm-80) cc_final: 0.6819 (ptm-80)
REVERT: A 1003 ARG cc_start: 0.7438 (ttm110) cc_final: 0.7166 (ttt90)
REVERT: A 1237 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.5877 (ttt180)
REVERT: A 1372 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6380 (tp)
  outliers start: 40
  outliers final: 22
  residues processed: 99
  average time/residue: 0.6173
  time to fit residues: 66.0709
Evaluate side-chains
  96 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 64
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  621 PHE
Chi-restraints excluded: chain A residue  626 SER
Chi-restraints excluded: chain A residue  653 GLU
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  741 GLN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  771 MET
Chi-restraints excluded: chain A residue  975 GLN
Chi-restraints excluded: chain A residue  992 ASP
Chi-restraints excluded: chain A residue 1004 ASP
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1214 THR
Chi-restraints excluded: chain A residue 1237 ARG
Chi-restraints excluded: chain A residue 1239 ILE
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1298 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1372 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 118 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   chunk 100 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 114 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 66 optimal weight:   10.0000
   chunk 96 optimal weight:    3.9990
   chunk 116 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 975 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.168243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.135425 restraints weight = 14369.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 1.85
r_work: 0.3235 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12431  Z= 0.151
  Angle     :  0.606  13.915  17464  Z= 0.312
  Chirality :  0.037   0.258   2022
  Planarity :  0.004   0.055   1674
  Dihedral  : 22.246 179.495   3319
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 28.42 %
    Favored  : 68.34 %
  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 are not related in a simple way.
  whole: -0.31 (0.26), residues: 1047
  helix:  0.74 (0.24), residues: 472
  sheet: -0.14 (0.87), residues: 42
  loop : -1.09 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1294 
 TYR   0.014   0.001   TYR A 788 
 PHE   0.019   0.002   PHE A 687 
 TRP   0.035   0.002   TRP A 307 
 HIS   0.005   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (12431)
  covalent geometry    : angle       0.60617 (17464)
  hydrogen bonds       : bond        0.04731 (  416)
  hydrogen bonds       : angle       4.40048 ( 1113)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 68
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.6091 (m-40) cc_final: 0.5613 (m110)
REVERT: A   85 GLN cc_start: 0.7702 (tt0) cc_final: 0.7346 (tp-100)
REVERT: A  105 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8482 (m)
REVERT: A  192 MET cc_start: 0.4189 (mpt) cc_final: 0.3726 (mpt)
REVERT: A  297 TYR cc_start: 0.6431 (m-80) cc_final: 0.5735 (t80)
REVERT: A  465 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7564 (mtm)
REVERT: A  653 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6587 (tp30)
REVERT: A  675 GLU cc_start: 0.5822 (OUTLIER) cc_final: 0.5451 (pp20)
REVERT: A  689 PHE cc_start: 0.6122 (OUTLIER) cc_final: 0.5000 (p90)
REVERT: A  741 GLN cc_start: 0.5827 (OUTLIER) cc_final: 0.5625 (mt0)
REVERT: A  992 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6676 (m-30)
REVERT: A  996 ARG cc_start: 0.7091 (ptm-80) cc_final: 0.6797 (ptm-80)
REVERT: A 1003 ARG cc_start: 0.7350 (ttm110) cc_final: 0.7085 (ttt90)
REVERT: A 1237 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.5796 (ttt180)
REVERT: A 1275 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7900 (ttp80)
REVERT: A 1372 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6305 (tp)
  outliers start: 31
  outliers final: 20
  residues processed: 92
  average time/residue: 0.6987
  time to fit residues: 69.4130
Evaluate side-chains
  94 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 65
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  621 PHE
Chi-restraints excluded: chain A residue  626 SER
Chi-restraints excluded: chain A residue  653 GLU
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  689 PHE
Chi-restraints excluded: chain A residue  741 GLN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  771 MET
Chi-restraints excluded: chain A residue  992 ASP
Chi-restraints excluded: chain A residue 1004 ASP
Chi-restraints excluded: chain A residue 1103 VAL
Chi-restraints excluded: chain A residue 1214 THR
Chi-restraints excluded: chain A residue 1237 ARG
Chi-restraints excluded: chain A residue 1239 ILE
Chi-restraints excluded: chain A residue 1277 THR
Chi-restraints excluded: chain A residue 1298 VAL
Chi-restraints excluded: chain A residue 1343 LEU
Chi-restraints excluded: chain A residue 1372 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 114 optimal weight:    6.9990
   chunk 69 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 975 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.167438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.136232 restraints weight = 14304.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 1.70
r_work: 0.3235 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12431  Z= 0.180
  Angle     :  0.628  13.346  17464  Z= 0.323
  Chirality :  0.038   0.260   2022
  Planarity :  0.004   0.055   1674
  Dihedral  : 22.244 179.220   3319
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 28.11 %
    Favored  : 68.44 %
  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 are not related in a simple way.
  whole: -0.38 (0.26), residues: 1047
  helix:  0.67 (0.24), residues: 473
  sheet: -0.49 (0.86), residues: 44
  loop : -1.08 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 994 
 TYR   0.017   0.002   TYR A 788 
 PHE   0.019   0.002   PHE A 687 
 TRP   0.035   0.002   TRP A 307 
 HIS   0.005   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (12431)
  covalent geometry    : angle       0.62849 (17464)
  hydrogen bonds       : bond        0.04866 (  416)
  hydrogen bonds       : angle       4.42715 ( 1113)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3200.91 seconds
wall clock time: 55 minutes 35.75 seconds (3335.75 seconds total)