Starting phenix.real_space_refine
on Wed Jul 30 08:39:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6o0z_0585/07_2025/6o0z_0585.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6o0z_0585/07_2025/6o0z_0585.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6o0z_0585/07_2025/6o0z_0585.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6o0z_0585/07_2025/6o0z_0585.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6o0z_0585/07_2025/6o0z_0585.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6o0z_0585/07_2025/6o0z_0585.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     134      5.49       5
     S      15      5.16       5
     C    7080      2.51       5
     N    2132      2.21       5
     O    2551      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11912
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9063
      Number of conformers: 1
      Conformer: "B"
        Number of residues, atoms: 1288, 9063
          Classifications: {'peptide': 1288}
          Incomplete info: {'truncation_to_alanine': 391}
          Link IDs: {'PTRANS': 34, 'TRANS': 1253}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 1545
          Unresolved non-hydrogen angles: 1919
          Unresolved non-hydrogen dihedrals: 1252
          Unresolved non-hydrogen chiralities: 106
          Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 3, 'TYR:plan': 12, 'ASN:plan1': 32, 'TRP:plan': 1, 'ASP:plan': 45, 'PHE:plan': 16, 'GLU:plan': 61, 'ARG:plan': 26}
          Unresolved non-hydrogen planarities: 883
    Chain: "B"
      Number of atoms: 2058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 2058
          Classifications: {'RNA': 96}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 34}
          Link IDs: {'rna2p': 11, 'rna3p': 84}
    Chain: "C"
      Number of atoms: 563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 563
          Classifications: {'DNA': 28}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 27}
    Chain: "D"
      Number of atoms: 228
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 228
          Classifications: {'DNA': 11}
          Link IDs: {'rna3p': 10}
  Time building chain proxies: 7.85, per 1000 atoms: 0.66
  Number of scatterers: 11912
  At special positions: 0
  Unit cell: (140.448, 127.072, 98.648, 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      15     16.00
     P     134     15.00
     O    2551      8.00
     N    2132      7.00
     C    7080      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: 3.00
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2460

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 7 sheets defined
      52.7% alpha, 6.3% beta
      49 base pairs and 89 stacking pairs defined.
    Time for finding SS restraints: 4.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 86
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 3.960A  pdb=" N   ALA A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 122 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 4.018A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.608A  pdb=" N   PHE A 164 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 196
      removed outlier: 3.592A  pdb=" N   ILE A 186 " --> pdb=" O   ASP A 182 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   GLN A 187 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL A 189 " --> pdb=" O   PHE A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
    Processing helix  chain 'A' and resid 218 through 227
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 238 through 245
    Processing helix  chain 'A' and resid 269 through 281
      removed outlier: 4.594A  pdb=" N   ASP A 273 " --> pdb=" O   ASP A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 302
    Processing helix  chain 'A' and resid 315 through 342
      removed outlier: 3.557A  pdb=" N   ALA A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 345
      No H-bonds generated for 'chain 'A' and resid 343 through 345'
    Processing helix  chain 'A' and resid 346 through 352
      removed outlier: 3.520A  pdb=" N   ILE A 350 " --> pdb=" O   LYS A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 383
      Proline residue:  A 378  - end of helix
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 411 through 426
      removed outlier: 4.352A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.628A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 446
      removed outlier: 3.572A  pdb=" N   ILE A 440 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 482
      removed outlier: 3.618A  pdb=" N   VAL A 481 " --> pdb=" O   ASN A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
      removed outlier: 3.676A  pdb=" N   SER A 487 " --> pdb=" O   ASP A 483 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ILE A 492 " --> pdb=" O   ALA A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 525
    Processing helix  chain 'A' and resid 543 through 556
      removed outlier: 4.275A  pdb=" N   ALA A 547 " --> pdb=" O   GLU A 543 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   PHE A 553 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   LYS A 554 " --> pdb=" O   ASP A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 573
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 605 through 609
      removed outlier: 3.524A  pdb=" N   ASP A 608 " --> pdb=" O   ASP A 605 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ASN A 609 " --> pdb=" O   PHE A 606 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 605 through 609'
    Processing helix  chain 'A' and resid 610 through 626
      removed outlier: 4.013A  pdb=" N   ASP A 614 " --> pdb=" O   GLU A 610 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU A 621 " --> pdb=" O   GLU A 617 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE A 626 " --> pdb=" O   THR A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 638
    Processing helix  chain 'A' and resid 644 through 653
    Processing helix  chain 'A' and resid 664 through 669
    Processing helix  chain 'A' and resid 678 through 685
      removed outlier: 3.602A  pdb=" N   SER A 685 " --> pdb=" O   ASP A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 698
    Processing helix  chain 'A' and resid 703 through 711
      removed outlier: 3.690A  pdb=" N   ASP A 707 " --> pdb=" O   THR A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 726
      removed outlier: 3.798A  pdb=" N   ASN A 726 " --> pdb=" O   GLU A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 3.545A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLY A 736 " --> pdb=" O   ALA A 732 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   MET A 751 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 792
      removed outlier: 3.562A  pdb=" N   GLY A 792 " --> pdb=" O   ILE A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 817
      removed outlier: 3.974A  pdb=" N   TYR A 812 " --> pdb=" O   ASN A 808 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   TYR A 814 " --> pdb=" O   LYS A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 851 through 853
      No H-bonds generated for 'chain 'A' and resid 851 through 853'
    Processing helix  chain 'A' and resid 872 through 879
    Processing helix  chain 'A' and resid 881 through 889
    Processing helix  chain 'A' and resid 893 through 902
    Processing helix  chain 'A' and resid 903 through 905
      No H-bonds generated for 'chain 'A' and resid 903 through 905'
    Processing helix  chain 'A' and resid 909 through 922
    Processing helix  chain 'A' and resid 925 through 940
      removed outlier: 3.857A  pdb=" N   LYS A 929 " --> pdb=" O   ARG A 925 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 971
      removed outlier: 4.131A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   PHE A 970 " --> pdb=" O   PHE A 966 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 1001
    Processing helix  chain 'A' and resid 1004 through 1009
      removed outlier: 3.870A  pdb=" N   PHE A1008 " --> pdb=" O   LEU A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1075 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1168 through 1177
      removed outlier: 3.747A  pdb=" N   ASN A1177 " --> pdb=" O   SER A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1186
      removed outlier: 3.690A  pdb=" N   PHE A1181 " --> pdb=" O   ASN A1177 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLY A1186 " --> pdb=" O   LEU A1182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1191 through 1195
      removed outlier: 4.029A  pdb=" N   ILE A1195 " --> pdb=" O   LYS A1192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1241
      removed outlier: 3.592A  pdb=" N   HIS A1241 " --> pdb=" O   TYR A1237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1261
    Processing helix  chain 'A' and resid 1264 through 1280
      removed outlier: 3.906A  pdb=" N   GLU A1268 " --> pdb=" O   HIS A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1302 through 1312
      removed outlier: 4.172A  pdb=" N   GLU A1307 " --> pdb=" O   ARG A1303 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ASN A1308 " --> pdb=" O   GLU A1304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1313 through 1315
      No H-bonds generated for 'chain 'A' and resid 1313 through 1315'
    Processing helix  chain 'A' and resid 1341 through 1344
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957
      removed outlier: 6.201A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL A1095 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32
    Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36
      removed outlier: 6.251A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 839 through 840
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1120 through 1121
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.760A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)

    441 hydrogen bonds defined for protein.
    1296 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      122 hydrogen bonds
      240 hydrogen bond angles
      0 basepair planarities
      49 basepair parallelities
      89 stacking parallelities
  Total time for adding SS restraints: 6.98

  Time building geometry restraints manager: 3.63 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: 2133
        1.33 -     1.45: 3597
        1.45 -     1.57: 6375
        1.57 -     1.69: 266
        1.69 -     1.81: 28
  Bond restraints: 12399
  Sorted by residual:
  bond pdb=" C   LEU A1198 "
       pdb=" O   LEU A1198 "
    ideal  model  delta    sigma   weight residual
    1.249  1.236  0.013 8.50e-03 1.38e+04 2.41e+00
  bond pdb=" O5'  DC C  20 "
       pdb=" C5'  DC C  20 "
    ideal  model  delta    sigma   weight residual
    1.423  1.379  0.044 3.00e-02 1.11e+03 2.11e+00
  bond pdb=" CG  LYS A1334 "
       pdb=" CD  LYS A1334 "
    ideal  model  delta    sigma   weight residual
    1.520  1.482  0.038 3.00e-02 1.11e+03 1.61e+00
  bond pdb=" C1'  DC C  20 "
       pdb=" N1   DC C  20 "
    ideal  model  delta    sigma   weight residual
    1.490  1.527 -0.037 3.00e-02 1.11e+03 1.49e+00
  bond pdb=" C   ILE A1110 "
       pdb=" N   LEU A1111 "
    ideal  model  delta    sigma   weight residual
    1.339  1.273  0.067 5.57e-02 3.22e+02 1.44e+00
  ... (remaining 12394 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 16848
        1.65 -     3.30: 536
        3.30 -     4.95: 59
        4.95 -     6.60: 20
        6.60 -     8.25: 8
  Bond angle restraints: 17471
  Sorted by residual:
  angle pdb=" C3'   A B  68 "
        pdb=" O3'   A B  68 "
        pdb=" P     A B  69 "
      ideal   model   delta    sigma   weight residual
     120.20  126.75   -6.55 1.50e+00 4.44e-01 1.90e+01
  angle pdb=" C   LYS A 862 "
        pdb=" N   ASN A 863 "
        pdb=" CA  ASN A 863 "
      ideal   model   delta    sigma   weight residual
     121.54  129.20   -7.66 1.91e+00 2.74e-01 1.61e+01
  angle pdb=" O3'   A B  68 "
        pdb=" C3'   A B  68 "
        pdb=" C2'   A B  68 "
      ideal   model   delta    sigma   weight residual
     113.70  119.68   -5.98 1.50e+00 4.44e-01 1.59e+01
  angle pdb=" CA  LYS A1334 "
        pdb=" CB  LYS A1334 "
        pdb=" CG  LYS A1334 "
      ideal   model   delta    sigma   weight residual
     114.10  107.11    6.99 2.00e+00 2.50e-01 1.22e+01
  angle pdb=" C3'   A B  42 "
        pdb=" O3'   A B  42 "
        pdb=" P     G B  43 "
      ideal   model   delta    sigma   weight residual
     120.20  125.37   -5.17 1.50e+00 4.44e-01 1.19e+01
  ... (remaining 17466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.56: 6972
       34.56 -    69.13: 393
       69.13 -   103.69: 27
      103.69 -   138.25: 0
      138.25 -   172.81: 3
  Dihedral angle restraints: 7395
    sinusoidal: 3618
      harmonic: 3777
  Sorted by residual:
  dihedral pdb=" O4'   C B  70 "
           pdb=" C1'   C B  70 "
           pdb=" N1    C B  70 "
           pdb=" C2    C B  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   43.08  156.92     1      1.50e+01 4.44e-03 8.19e+01
  dihedral pdb=" CA  ASP A 861 "
           pdb=" C   ASP A 861 "
           pdb=" N   LYS A 862 "
           pdb=" CA  LYS A 862 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.81   22.19     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  SER A1040 "
           pdb=" C   SER A1040 "
           pdb=" N   ASN A1041 "
           pdb=" CA  ASN A1041 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.30  -20.70     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 7392 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1835
       0.062 -    0.123: 261
       0.123 -    0.185: 28
       0.185 -    0.247: 2
       0.247 -    0.309: 2
  Chirality restraints: 2128
  Sorted by residual:
  chirality pdb=" C3'   A B  42 "
            pdb=" C4'   A B  42 "
            pdb=" O3'   A B  42 "
            pdb=" C2'   A B  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.17   -0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" C3'   A B  38 "
            pdb=" C4'   A B  38 "
            pdb=" O3'   A B  38 "
            pdb=" C2'   A B  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.22   -0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CB  VAL A1149 "
            pdb=" CA  VAL A1149 "
            pdb=" CG1 VAL A1149 "
            pdb=" CG2 VAL A1149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.10e-01
  ... (remaining 2125 not shown)

  Planarity restraints: 1752
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 474 "   -0.035 5.00e-02 4.00e+02   5.19e-02 4.31e+00
        pdb=" N   PRO A 475 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 475 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 475 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1228 "   -0.034 5.00e-02 4.00e+02   5.09e-02 4.14e+00
        pdb=" N   PRO A1229 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A1229 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A1229 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A1342 "   -0.009 2.00e-02 2.50e+03   1.88e-02 3.53e+00
        pdb=" C   VAL A1342 "    0.033 2.00e-02 2.50e+03
        pdb=" O   VAL A1342 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A1343 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1749 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3643
        2.82 -     3.34: 9736
        3.34 -     3.86: 20451
        3.86 -     4.38: 21925
        4.38 -     4.90: 35065
  Nonbonded interactions: 90820
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 469 "
            pdb=" OE1 GLU A 471 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   TYR A 521 "
            pdb=" OG1 THR A 525 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   LYS A 141 "
            pdb=" OG  SER A 145 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OG  SER A1109 "
            pdb=" OP2  DG C  11 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" N2    G B  73 "
            pdb=" OP2   A B  76 "
     model   vdw
     2.337 3.120
  ... (remaining 90815 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.49 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:             13.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     36.390
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.060
  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:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
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      :  0.006   0.067  12399  Z= 0.264
  Angle     :  0.716   8.255  17471  Z= 0.395
  Chirality :  0.044   0.309   2128
  Planarity :  0.005   0.052   1752
  Dihedral  : 18.936 172.814   4935
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  8.34 %
    Favored  : 91.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.11 (0.18), residues: 1264
  helix: -2.68 (0.15), residues: 608
  sheet: -0.72 (0.46), residues: 127
  loop : -3.20 (0.21), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A 167 
 PHE   0.016   0.002   PHE A1324 
 TYR   0.014   0.002   TYR A 325 
 ARG   0.005   0.000   ARG A1084 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13168 (  563)
  hydrogen bonds       : angle       6.24808 ( 1536)
  covalent geometry    : bond        0.00565 (12399)
  covalent geometry    : angle       0.71644 (17471)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 1.267 
Fit side-chains
REVERT: A  518 PHE cc_start: 0.9042 (t80) cc_final: 0.8744 (t80)
REVERT: A  927 ILE cc_start: 0.9262 (mt) cc_final: 0.9034 (tp)
REVERT: A  933 GLN cc_start: 0.9239 (tt0) cc_final: 0.9036 (tm-30)
REVERT: A  961 LYS cc_start: 0.8817 (tptp) cc_final: 0.8564 (tptp)
REVERT: A 1183 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8333 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 72
  average time/residue: 0.2962
  time to fit residues: 30.7499
Evaluate side-chains
  52 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1098 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    9.9990
   chunk 106 optimal weight:    0.9990
   chunk 58 optimal weight:    8.9990
   chunk 36 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 56 optimal weight:   10.0000
   chunk 109 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 66 optimal weight:   50.0000
   chunk 81 optimal weight:    7.9990
   chunk 127 optimal weight:    4.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A 113 HIS
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 420 HIS
A 426 GLN
A 990 ASN
A1272 GLN
A1308 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.086337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.058095 restraints weight = 35706.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 2.96
r_work: 0.2740 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2734
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2734 r_free = 0.2734    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.0933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12399  Z= 0.165
  Angle     :  0.507   5.943  17471  Z= 0.280
  Chirality :  0.036   0.202   2128
  Planarity :  0.004   0.059   1752
  Dihedral  : 19.835 177.699   3226
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  9.71 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.22), residues: 1264
  helix: -0.63 (0.20), residues: 625
  sheet: -0.48 (0.47), residues: 127
  loop : -2.87 (0.23), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1074 
 HIS   0.003   0.001   HIS A 160 
 PHE   0.009   0.001   PHE A 432 
 TYR   0.010   0.001   TYR A 325 
 ARG   0.006   0.000   ARG A 976 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04494 (  563)
  hydrogen bonds       : angle       4.37983 ( 1536)
  covalent geometry    : bond        0.00350 (12399)
  covalent geometry    : angle       0.50702 (17471)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 1.207 
Fit side-chains
REVERT: A  927 ILE cc_start: 0.9253 (mt) cc_final: 0.9009 (tp)
  outliers start: 10
  outliers final: 6
  residues processed: 64
  average time/residue: 0.1900
  time to fit residues: 20.0334
Evaluate side-chains
  53 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue 1098 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 79 optimal weight:   50.0000
   chunk 1 optimal weight:    7.9990
   chunk 135 optimal weight:   10.0000
   chunk 110 optimal weight:    0.9980
   chunk 78 optimal weight:   20.0000
   chunk 75 optimal weight:   50.0000
   chunk 91 optimal weight:    6.9990
   chunk 102 optimal weight:    0.7980
   chunk 76 optimal weight:   40.0000
   chunk 109 optimal weight:    0.9990
   overall best weight:    3.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 990 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.085234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.056313 restraints weight = 36475.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.2841 rms_B_bonded: 2.93
r_work: 0.2701 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2698
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2698 r_free = 0.2698    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.98   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2698 r_free = 0.2698    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8822
moved from start:          0.1167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  12399  Z= 0.233
  Angle     :  0.546   6.459  17471  Z= 0.294
  Chirality :  0.038   0.197   2128
  Planarity :  0.003   0.058   1752
  Dihedral  : 19.797 173.937   3226
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 12.31 %
    Favored  : 86.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.23), residues: 1264
  helix:  0.34 (0.21), residues: 617
  sheet: -0.68 (0.47), residues: 137
  loop : -2.54 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1074 
 HIS   0.003   0.001   HIS A 167 
 PHE   0.011   0.001   PHE A 518 
 TYR   0.012   0.001   TYR A 325 
 ARG   0.003   0.000   ARG A 976 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04894 (  563)
  hydrogen bonds       : angle       4.24152 ( 1536)
  covalent geometry    : bond        0.00509 (12399)
  covalent geometry    : angle       0.54584 (17471)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 1.183 
Fit side-chains
REVERT: A  631 MET cc_start: 0.9374 (mpp) cc_final: 0.9114 (pmm)
REVERT: A  927 ILE cc_start: 0.9329 (mt) cc_final: 0.9099 (tp)
  outliers start: 10
  outliers final: 7
  residues processed: 57
  average time/residue: 0.2150
  time to fit residues: 20.1681
Evaluate side-chains
  53 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   95 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue 1098 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 97 optimal weight:   50.0000
   chunk 136 optimal weight:    8.9990
   chunk 131 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9980
   chunk 78 optimal weight:   30.0000
   chunk 1 optimal weight:    6.9990
   chunk 77 optimal weight:   40.0000
   chunk 87 optimal weight:    0.9990
   chunk 120 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 723 HIS
A 990 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.085625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.056767 restraints weight = 36185.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 2.90
r_work: 0.2708 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8811
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12399  Z= 0.207
  Angle     :  0.522   6.264  17471  Z= 0.282
  Chirality :  0.037   0.189   2128
  Planarity :  0.003   0.057   1752
  Dihedral  : 19.755 171.626   3226
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.95 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.24), residues: 1264
  helix:  0.82 (0.22), residues: 615
  sheet: -0.59 (0.47), residues: 137
  loop : -2.39 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1074 
 HIS   0.003   0.001   HIS A 160 
 PHE   0.011   0.001   PHE A 432 
 TYR   0.014   0.001   TYR A 271 
 ARG   0.002   0.000   ARG A1078 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04562 (  563)
  hydrogen bonds       : angle       4.09869 ( 1536)
  covalent geometry    : bond        0.00450 (12399)
  covalent geometry    : angle       0.52178 (17471)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 1.143 
Fit side-chains
REVERT: A  927 ILE cc_start: 0.9325 (mt) cc_final: 0.9098 (tp)
  outliers start: 15
  outliers final: 11
  residues processed: 63
  average time/residue: 0.2166
  time to fit residues: 22.8636
Evaluate side-chains
  57 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   95 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1098 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 8 optimal weight:    0.0970
   chunk 99 optimal weight:   20.0000
   chunk 123 optimal weight:    0.7980
   chunk 82 optimal weight:    8.9990
   chunk 103 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0040
   chunk 114 optimal weight:    6.9990
   chunk 105 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 136 optimal weight:    8.9990
   overall best weight:    1.1794

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.087347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.059213 restraints weight = 35890.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 2.95
r_work: 0.2765 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12399  Z= 0.109
  Angle     :  0.460   5.930  17471  Z= 0.250
  Chirality :  0.035   0.169   2128
  Planarity :  0.003   0.054   1752
  Dihedral  : 19.602 172.105   3226
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 14.91 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.25), residues: 1264
  helix:  1.24 (0.22), residues: 613
  sheet: -0.34 (0.48), residues: 137
  loop : -2.09 (0.26), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1074 
 HIS   0.002   0.000   HIS A 160 
 PHE   0.022   0.001   PHE A 518 
 TYR   0.010   0.001   TYR A 271 
 ARG   0.002   0.000   ARG A1078 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03490 (  563)
  hydrogen bonds       : angle       3.74270 ( 1536)
  covalent geometry    : bond        0.00230 (12399)
  covalent geometry    : angle       0.46043 (17471)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: A  631 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8779 (pmm)
REVERT: A  925 ARG cc_start: 0.7515 (mtp180) cc_final: 0.7311 (mtm180)
REVERT: A  927 ILE cc_start: 0.9252 (mt) cc_final: 0.8993 (tp)
REVERT: A 1169 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7663 (mtp)
  outliers start: 12
  outliers final: 9
  residues processed: 63
  average time/residue: 0.1976
  time to fit residues: 20.4862
Evaluate side-chains
  59 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   95 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  631 MET
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue 1098 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1169 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 72 optimal weight:   50.0000
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 122 optimal weight:    0.0370
   chunk 23 optimal weight:   40.0000
   chunk 35 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9980
   chunk 108 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    2.4062

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.086301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.058259 restraints weight = 36242.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 2.95
r_work: 0.2732 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2727
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2727
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12399  Z= 0.172
  Angle     :  0.492   6.567  17471  Z= 0.265
  Chirality :  0.036   0.175   2128
  Planarity :  0.003   0.054   1752
  Dihedral  : 19.616 170.792   3226
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 13.82 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.25), residues: 1264
  helix:  1.37 (0.22), residues: 616
  sheet: -0.34 (0.48), residues: 136
  loop : -2.06 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1074 
 HIS   0.003   0.001   HIS A 160 
 PHE   0.011   0.001   PHE A 432 
 TYR   0.011   0.001   TYR A 271 
 ARG   0.002   0.000   ARG A1078 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04096 (  563)
  hydrogen bonds       : angle       3.81201 ( 1536)
  covalent geometry    : bond        0.00375 (12399)
  covalent geometry    : angle       0.49192 (17471)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 49
  time to evaluate  : 1.217 
Fit side-chains
REVERT: A  927 ILE cc_start: 0.9291 (mt) cc_final: 0.9067 (tp)
REVERT: A 1169 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7827 (mtp)
  outliers start: 18
  outliers final: 14
  residues processed: 64
  average time/residue: 0.1974
  time to fit residues: 20.7547
Evaluate side-chains
  64 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   95 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1098 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1169 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:   10.0000
   chunk 67 optimal weight:    9.9990
   chunk 116 optimal weight:    0.0040
   chunk 36 optimal weight:    4.9990
   chunk 103 optimal weight:    5.9990
   chunk 131 optimal weight:   10.0000
   chunk 57 optimal weight:   40.0000
   chunk 28 optimal weight:   10.0000
   chunk 23 optimal weight:   50.0000
   chunk 138 optimal weight:    5.9990
   chunk 129 optimal weight:    5.9990
   overall best weight:    4.6000

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.084318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.055572 restraints weight = 36899.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 2.94
r_work: 0.2681 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8842
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064  12399  Z= 0.308
  Angle     :  0.599   8.923  17471  Z= 0.318
  Chirality :  0.040   0.197   2128
  Planarity :  0.003   0.056   1752
  Dihedral  : 19.753 168.167   3226
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.50 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.24), residues: 1264
  helix:  1.18 (0.22), residues: 619
  sheet: -0.44 (0.48), residues: 137
  loop : -2.19 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1074 
 HIS   0.004   0.001   HIS A 167 
 PHE   0.009   0.001   PHE A 432 
 TYR   0.015   0.001   TYR A 271 
 ARG   0.002   0.000   ARG A1084 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05451 (  563)
  hydrogen bonds       : angle       4.22846 ( 1536)
  covalent geometry    : bond        0.00672 (12399)
  covalent geometry    : angle       0.59941 (17471)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 51
  time to evaluate  : 1.258 
Fit side-chains
REVERT: A  927 ILE cc_start: 0.9366 (mt) cc_final: 0.9106 (tp)
  outliers start: 19
  outliers final: 16
  residues processed: 67
  average time/residue: 0.1950
  time to fit residues: 21.3641
Evaluate side-chains
  61 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 45
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   95 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  631 MET
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1098 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 25 optimal weight:   50.0000
   chunk 32 optimal weight:    6.9990
   chunk 98 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 47 optimal weight:    0.6980
   chunk 50 optimal weight:    6.9990
   chunk 134 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.085357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.057177 restraints weight = 36351.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 2.95
r_work: 0.2716 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12399  Z= 0.184
  Angle     :  0.513   6.219  17471  Z= 0.276
  Chirality :  0.037   0.186   2128
  Planarity :  0.003   0.054   1752
  Dihedral  : 19.676 168.757   3226
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 15.18 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.25), residues: 1264
  helix:  1.32 (0.22), residues: 623
  sheet: -0.35 (0.48), residues: 136
  loop : -2.05 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1074 
 HIS   0.003   0.001   HIS A 160 
 PHE   0.011   0.001   PHE A1174 
 TYR   0.012   0.001   TYR A 271 
 ARG   0.001   0.000   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04388 (  563)
  hydrogen bonds       : angle       3.95693 ( 1536)
  covalent geometry    : bond        0.00400 (12399)
  covalent geometry    : angle       0.51284 (17471)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 1.048 
Fit side-chains
REVERT: A  927 ILE cc_start: 0.9299 (mt) cc_final: 0.9082 (tp)
  outliers start: 14
  outliers final: 12
  residues processed: 60
  average time/residue: 0.1979
  time to fit residues: 19.4639
Evaluate side-chains
  60 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   95 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1098 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 24 optimal weight:   50.0000
   chunk 58 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 129 optimal weight:    5.9990
   chunk 77 optimal weight:   50.0000
   chunk 53 optimal weight:   40.0000
   chunk 125 optimal weight:    7.9990
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.083991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.055330 restraints weight = 36802.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.2817 rms_B_bonded: 2.93
r_work: 0.2677 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8845
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063  12399  Z= 0.326
  Angle     :  0.612   8.507  17471  Z= 0.325
  Chirality :  0.040   0.202   2128
  Planarity :  0.003   0.056   1752
  Dihedral  : 19.784 167.551   3226
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.73 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.24), residues: 1264
  helix:  1.19 (0.22), residues: 617
  sheet: -0.48 (0.48), residues: 137
  loop : -2.17 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1074 
 HIS   0.004   0.001   HIS A 167 
 PHE   0.023   0.002   PHE A 518 
 TYR   0.015   0.002   TYR A 271 
 ARG   0.006   0.000   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05477 (  563)
  hydrogen bonds       : angle       4.28162 ( 1536)
  covalent geometry    : bond        0.00713 (12399)
  covalent geometry    : angle       0.61190 (17471)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 1.527 
Fit side-chains
REVERT: A  927 ILE cc_start: 0.9368 (mt) cc_final: 0.9114 (tp)
  outliers start: 15
  outliers final: 14
  residues processed: 59
  average time/residue: 0.2430
  time to fit residues: 23.3742
Evaluate side-chains
  59 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   95 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  631 MET
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1098 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 133 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 118 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0040
   chunk 86 optimal weight:    2.9990
   chunk 94 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 112 optimal weight:    0.3980
   chunk 10 optimal weight:    0.8980
   chunk 111 optimal weight:    4.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.087820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.060391 restraints weight = 35957.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.2925 rms_B_bonded: 2.95
r_work: 0.2780 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2774
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2774
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12399  Z= 0.100
  Angle     :  0.479   7.776  17471  Z= 0.257
  Chirality :  0.035   0.171   2128
  Planarity :  0.003   0.051   1752
  Dihedral  : 19.566 170.021   3226
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.42 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.25), residues: 1264
  helix:  1.62 (0.22), residues: 615
  sheet: -0.16 (0.48), residues: 136
  loop : -1.90 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 464 
 HIS   0.003   0.001   HIS A 982 
 PHE   0.012   0.001   PHE A1174 
 TYR   0.010   0.001   TYR A1237 
 ARG   0.001   0.000   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03338 (  563)
  hydrogen bonds       : angle       3.69292 ( 1536)
  covalent geometry    : bond        0.00208 (12399)
  covalent geometry    : angle       0.47886 (17471)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 1.142 
Fit side-chains
REVERT: A  271 TYR cc_start: 0.6903 (t80) cc_final: 0.6435 (t80)
REVERT: A  927 ILE cc_start: 0.9256 (mt) cc_final: 0.9029 (tp)
  outliers start: 13
  outliers final: 13
  residues processed: 64
  average time/residue: 0.2040
  time to fit residues: 21.4743
Evaluate side-chains
  62 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   95 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  631 MET
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1098 THR
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 132 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0370
   chunk 37 optimal weight:    7.9990
   chunk 27 optimal weight:   20.0000
   chunk 96 optimal weight:    0.7980
   chunk 114 optimal weight:   10.0000
   overall best weight:    1.3664

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.087576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.059269 restraints weight = 35925.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 2.91
r_work: 0.2758 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2754
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2754 r_free = 0.2754    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2754 r_free = 0.2754    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2754
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12399  Z= 0.120
  Angle     :  0.470   8.742  17471  Z= 0.253
  Chirality :  0.035   0.171   2128
  Planarity :  0.003   0.053   1752
  Dihedral  : 19.555 169.844   3226
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.83 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.25), residues: 1264
  helix:  1.71 (0.22), residues: 618
  sheet: -0.12 (0.48), residues: 136
  loop : -1.84 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1074 
 HIS   0.002   0.000   HIS A 328 
 PHE   0.024   0.001   PHE A 518 
 TYR   0.009   0.001   TYR A 271 
 ARG   0.002   0.000   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03550 (  563)
  hydrogen bonds       : angle       3.62960 ( 1536)
  covalent geometry    : bond        0.00259 (12399)
  covalent geometry    : angle       0.47031 (17471)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6931.65 seconds
wall clock time: 123 minutes 42.03 seconds (7422.03 seconds total)