Starting phenix.real_space_refine
on Thu Jun 12 19:46:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7z4j_14499/06_2025/7z4j_14499.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z4j_14499/06_2025/7z4j_14499.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7z4j_14499/06_2025/7z4j_14499.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z4j_14499/06_2025/7z4j_14499.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z4j_14499/06_2025/7z4j_14499.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z4j_14499/06_2025/7z4j_14499.cif"
  }
  resolution = 2.99
  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=   0.002 sd=   0.010
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: 6
    Type Number    sf(0)   Gaussians
     P     138      5.49       5
     Mg      4      5.21       5
     S      22      5.16       5
     C    8344      2.51       5
     N    2443      2.21       5
     O    2997      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13948
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 2081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2081
          Classifications: {'DNA': 1, 'RNA': 97}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 33}
          Link IDs: {'rna2p': 12, 'rna3p': 85}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'  G%5*END:plan2': 1, '  G%5*END:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "c"
      Number of atoms: 263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 263
          Classifications: {'DNA': 13}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 12}
    Chain: "C"
      Number of atoms: 324
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 324
          Classifications: {'DNA': 17}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 16}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {' DG%5*END:plan2': 1, ' DG%5*END:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "D"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 269
          Classifications: {'DNA': 14}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 13}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 10999
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1345, 10999
          Classifications: {'peptide': 1345}
          Link IDs: {'PTRANS': 35, 'TRANS': 1309}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 9.71, per 1000 atoms: 0.70
  Number of scatterers: 13948
  At special positions: 0
  Unit cell: (85.15, 119.6, 120.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      22     16.00
     P     138     15.00
     Mg      4     11.99
     O    2997      8.00
     N    2443      7.00
     C    8344      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: 4.10
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2556

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 10 sheets defined
      55.7% alpha, 9.7% beta
      50 base pairs and 80 stacking pairs defined.
    Time for finding SS restraints: 5.78
  Creating SS restraints...
    Processing helix  chain 'B' and resid 59 through 94
      removed outlier: 4.818A  pdb=" N   ASN B  88 " --> pdb=" O   GLU B  84 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   GLU B  89 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LYS B  92 " --> pdb=" O   ASN B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 104
    Processing helix  chain 'B' and resid 121 through 132
    Processing helix  chain 'B' and resid 134 through 145
      removed outlier: 3.706A  pdb=" N   LEU B 138 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 164
    Processing helix  chain 'B' and resid 181 through 196
      removed outlier: 3.835A  pdb=" N   LEU B 195 " --> pdb=" O   THR B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 213
    Processing helix  chain 'B' and resid 217 through 229
    Processing helix  chain 'B' and resid 236 through 247
    Processing helix  chain 'B' and resid 252 through 257
      removed outlier: 3.600A  pdb=" N   PHE B 256 " --> pdb=" O   PHE B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 282
    Processing helix  chain 'B' and resid 283 through 285
      No H-bonds generated for 'chain 'B' and resid 283 through 285'
    Processing helix  chain 'B' and resid 286 through 307
    Processing helix  chain 'B' and resid 315 through 343
    Processing helix  chain 'B' and resid 346 through 352
    Processing helix  chain 'B' and resid 358 through 364
    Processing helix  chain 'B' and resid 368 through 382
      Proline residue:  B 378  - end of helix
    Processing helix  chain 'B' and resid 386 through 395
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 3.810A  pdb=" N   ASN B 407 " --> pdb=" O   THR B 404 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   GLY B 408 " --> pdb=" O   PHE B 405 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER B 409 " --> pdb=" O   ASP B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 427
      removed outlier: 4.157A  pdb=" N   HIS B 415 " --> pdb=" O   PRO B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 435
    Processing helix  chain 'B' and resid 436 through 446
    Processing helix  chain 'B' and resid 477 through 481
      removed outlier: 3.545A  pdb=" N   VAL B 481 " --> pdb=" O   PHE B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 494
    Processing helix  chain 'B' and resid 512 through 526
      removed outlier: 3.997A  pdb=" N   LYS B 526 " --> pdb=" O   ASN B 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 541 through 552
    Processing helix  chain 'B' and resid 560 through 567
    Processing helix  chain 'B' and resid 591 through 602
    Processing helix  chain 'B' and resid 603 through 609
      removed outlier: 3.622A  pdb=" N   LEU B 607 " --> pdb=" O   ASP B 603 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 626
    Processing helix  chain 'B' and resid 628 through 637
    Processing helix  chain 'B' and resid 638 through 640
      No H-bonds generated for 'chain 'B' and resid 638 through 640'
    Processing helix  chain 'B' and resid 644 through 654
    Processing helix  chain 'B' and resid 664 through 668
    Processing helix  chain 'B' and resid 678 through 685
    Processing helix  chain 'B' and resid 692 through 698
    Processing helix  chain 'B' and resid 703 through 712
    Processing helix  chain 'B' and resid 713 through 715
      No H-bonds generated for 'chain 'B' and resid 713 through 715'
    Processing helix  chain 'B' and resid 719 through 727
    Processing helix  chain 'B' and resid 731 through 751
      removed outlier: 4.385A  pdb=" N   LYS B 735 " --> pdb=" O   PRO B 731 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLY B 736 " --> pdb=" O   ALA B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 769 through 776
    Processing helix  chain 'B' and resid 779 through 792
      removed outlier: 3.550A  pdb=" N   ARG B 783 " --> pdb=" O   GLU B 779 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 794 through 799
    Processing helix  chain 'B' and resid 804 through 807
    Processing helix  chain 'B' and resid 808 through 817
    Processing helix  chain 'B' and resid 851 through 853
      No H-bonds generated for 'chain 'B' and resid 851 through 853'
    Processing helix  chain 'B' and resid 860 through 867
    Processing helix  chain 'B' and resid 872 through 889
      removed outlier: 5.303A  pdb=" N   ASN B 881 " --> pdb=" O   LYS B 877 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   TYR B 882 " --> pdb=" O   LYS B 878 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 893 through 901
    Processing helix  chain 'B' and resid 902 through 904
      No H-bonds generated for 'chain 'B' and resid 902 through 904'
    Processing helix  chain 'B' and resid 909 through 915
      removed outlier: 4.417A  pdb=" N   GLY B 915 " --> pdb=" O   ASP B 912 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 917 through 940
      removed outlier: 4.012A  pdb=" N   LEU B 921 " --> pdb=" O   ILE B 917 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   VAL B 922 " --> pdb=" O   LYS B 918 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 960 through 970
    Processing helix  chain 'B' and resid 980 through 1001
      removed outlier: 4.458A  pdb=" N   ALA B 984 " --> pdb=" O   ASN B 980 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1004 through 1009
    Processing helix  chain 'B' and resid 1030 through 1043
      removed outlier: 4.309A  pdb=" N   MET B1043 " --> pdb=" O   TYR B1039 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1044 through 1047
    Processing helix  chain 'B' and resid 1078 through 1088
    Processing helix  chain 'B' and resid 1127 through 1132
    Processing helix  chain 'B' and resid 1170 through 1177
    Processing helix  chain 'B' and resid 1177 through 1186
    Processing helix  chain 'B' and resid 1229 through 1240
    Processing helix  chain 'B' and resid 1248 through 1262
    Processing helix  chain 'B' and resid 1263 through 1280
      removed outlier: 4.326A  pdb=" N   ASP B1267 " --> pdb=" O   LYS B1263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1283 through 1297
    Processing helix  chain 'B' and resid 1301 through 1313
    Processing helix  chain 'B' and resid 1314 through 1317
      removed outlier: 3.575A  pdb=" N   ASN B1317 " --> pdb=" O   THR B1314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1314 through 1317'
    Processing helix  chain 'B' and resid 1340 through 1344
    Processing helix  chain 'B' and resid 1363 through 1365
      No H-bonds generated for 'chain 'B' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 959
      removed outlier: 4.632A  pdb=" N   ILE B  11 " --> pdb=" O   GLU B 762 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46
      removed outlier: 9.929A  pdb=" N   GLU B1357 " --> pdb=" O   LYS B  31 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LYS B  33 " --> pdb=" O   GLU B1357 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   ARG B1359 " --> pdb=" O   LYS B  33 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   LEU B  35 " --> pdb=" O   ARG B1359 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   ASP B1361 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LEU B1203 " --> pdb=" O   ILE B1348 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   GLU B1219 " --> pdb=" O   ALA B1215 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509
      removed outlier: 5.621A  pdb=" N   LEU B 662 " --> pdb=" O   LEU B 508 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539
    Processing sheet with id=AA5, first strand: chain 'B' and resid 836 through 840
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1049 through 1050
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1063 through 1065
      removed outlier: 3.881A  pdb=" N   TRP B1074 " --> pdb=" O   GLU B1064 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1156 through 1163
      removed outlier: 7.224A  pdb=" N   ILE B1166 " --> pdb=" O   ALA B1140 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 1156 through 1163
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326

    536 hydrogen bonds defined for protein.
    1548 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      123 hydrogen bonds
      238 hydrogen bond angles
      0 basepair planarities
      50 basepair parallelities
      80 stacking parallelities
  Total time for adding SS restraints: 8.30

  Time building geometry restraints manager: 4.84 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: 2474
        1.33 -     1.45: 4187
        1.45 -     1.57: 7502
        1.57 -     1.69: 276
        1.69 -     1.81: 42
  Bond restraints: 14481
  Sorted by residual:
  bond pdb=" C   ARG B1333 "
       pdb=" O   ARG B1333 "
    ideal  model  delta    sigma   weight residual
    1.235  1.254 -0.019 1.21e-02 6.83e+03 2.56e+00
  bond pdb=" O5'  DC C  17 "
       pdb=" C5'  DC C  17 "
    ideal  model  delta    sigma   weight residual
    1.423  1.375  0.048 3.00e-02 1.11e+03 2.56e+00
  bond pdb=" C4'  DG C  16 "
       pdb=" C3'  DG C  16 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.029 2.00e-02 2.50e+03 2.05e+00
  bond pdb=" O5'  DC C  10 "
       pdb=" C5'  DC C  10 "
    ideal  model  delta    sigma   weight residual
    1.423  1.382  0.041 3.00e-02 1.11e+03 1.85e+00
  bond pdb=" C4'  DA C   8 "
       pdb=" C3'  DA C   8 "
    ideal  model  delta    sigma   weight residual
    1.523  1.498  0.025 2.00e-02 2.50e+03 1.61e+00
  ... (remaining 14476 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 19848
        1.55 -     3.10: 274
        3.10 -     4.65: 22
        4.65 -     6.20: 1
        6.20 -     7.75: 1
  Bond angle restraints: 20146
  Sorted by residual:
  angle pdb=" CA  LEU B1312 "
        pdb=" CB  LEU B1312 "
        pdb=" CG  LEU B1312 "
      ideal   model   delta    sigma   weight residual
     116.30  124.05   -7.75 3.50e+00 8.16e-02 4.90e+00
  angle pdb=" C2'   U A  59 "
        pdb=" C1'   U A  59 "
        pdb=" N1    U A  59 "
      ideal   model   delta    sigma   weight residual
     114.00  110.68    3.32 1.50e+00 4.44e-01 4.89e+00
  angle pdb=" C2'   U A  23 "
        pdb=" C1'   U A  23 "
        pdb=" N1    U A  23 "
      ideal   model   delta    sigma   weight residual
     112.00  114.97   -2.97 1.50e+00 4.44e-01 3.91e+00
  angle pdb=" C2'   G A  54 "
        pdb=" C1'   G A  54 "
        pdb=" N9    G A  54 "
      ideal   model   delta    sigma   weight residual
     112.00  114.81   -2.81 1.50e+00 4.44e-01 3.50e+00
  angle pdb=" NE  ARG B1333 "
        pdb=" CZ  ARG B1333 "
        pdb=" NH1 ARG B1333 "
      ideal   model   delta    sigma   weight residual
     121.50  119.73    1.77 1.00e+00 1.00e+00 3.12e+00
  ... (remaining 20141 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.77: 7965
       19.77 -    39.53: 520
       39.53 -    59.30: 228
       59.30 -    79.07: 79
       79.07 -    98.83: 6
  Dihedral angle restraints: 8798
    sinusoidal: 4846
      harmonic: 3952
  Sorted by residual:
  dihedral pdb=" O4'   G A  82 "
           pdb=" C1'   G A  82 "
           pdb=" N9    G A  82 "
           pdb=" C4    G A  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
      70.00   15.72   54.28     1      2.00e+01 2.50e-03 9.99e+00
  dihedral pdb=" N   ARG B 653 "
           pdb=" CA  ARG B 653 "
           pdb=" CB  ARG B 653 "
           pdb=" CG  ARG B 653 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.38   59.38     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" O5'   C A  91 "
           pdb=" C5'   C A  91 "
           pdb=" C4'   C A  91 "
           pdb=" C3'   C A  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -65.00 -123.58   58.58     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 8795 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1409
       0.028 -    0.056: 604
       0.056 -    0.083: 203
       0.083 -    0.111: 66
       0.111 -    0.139: 23
  Chirality restraints: 2305
  Sorted by residual:
  chirality pdb=" C1'   A A  51 "
            pdb=" O4'   A A  51 "
            pdb=" C2'   A A  51 "
            pdb=" N9    A A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.32    0.14 2.00e-01 2.50e+01 4.83e-01
  chirality pdb=" C3'  DC c  -1 "
            pdb=" C4'  DC c  -1 "
            pdb=" O3'  DC c  -1 "
            pdb=" C2'  DC c  -1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.52   -0.14 2.00e-01 2.50e+01 4.83e-01
  chirality pdb=" CA  VAL B 870 "
            pdb=" N   VAL B 870 "
            pdb=" C   VAL B 870 "
            pdb=" CB  VAL B 870 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.65e-01
  ... (remaining 2302 not shown)

  Planarity restraints: 2070
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U A  59 "    0.019 2.00e-02 2.50e+03   1.16e-02 3.04e+00
        pdb=" N1    U A  59 "   -0.029 2.00e-02 2.50e+03
        pdb=" C2    U A  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2    U A  59 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    U A  59 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    U A  59 "    0.004 2.00e-02 2.50e+03
        pdb=" O4    U A  59 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    U A  59 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    U A  59 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U A  23 "   -0.020 2.00e-02 2.50e+03   1.12e-02 2.83e+00
        pdb=" N1    U A  23 "    0.026 2.00e-02 2.50e+03
        pdb=" C2    U A  23 "    0.000 2.00e-02 2.50e+03
        pdb=" O2    U A  23 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    U A  23 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    U A  23 "   -0.005 2.00e-02 2.50e+03
        pdb=" O4    U A  23 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    U A  23 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    U A  23 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A  54 "    0.022 2.00e-02 2.50e+03   9.66e-03 2.80e+00
        pdb=" N9    G A  54 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8    G A  54 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G A  54 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    G A  54 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G A  54 "    0.002 2.00e-02 2.50e+03
        pdb=" O6    G A  54 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G A  54 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    G A  54 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G A  54 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G A  54 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    G A  54 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 2067 not shown)

  Histogram of nonbonded interaction distances:
        1.86 -     2.47: 98
        2.47 -     3.08: 9436
        3.08 -     3.68: 22427
        3.68 -     4.29: 33800
        4.29 -     4.90: 53227
  Nonbonded interactions: 118988
  Sorted by model distance:
  nonbonded pdb=" OP2  DT C   4 "
            pdb="MG    MG B1403 "
     model   vdw
     1.860 2.170
  nonbonded pdb=" OP1  DT D  -3 "
            pdb="MG    MG B1401 "
     model   vdw
     1.889 2.170
  nonbonded pdb="MG    MG A 201 "
            pdb=" O   HOH A 303 "
     model   vdw
     1.907 2.170
  nonbonded pdb="MG    MG B1403 "
            pdb=" O   HOH B1501 "
     model   vdw
     1.932 2.170
  nonbonded pdb="MG    MG A 201 "
            pdb=" O   HOH A 306 "
     model   vdw
     1.937 2.170
  ... (remaining 118983 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:             5.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.690
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     43.660
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   62.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14481  Z= 0.225
  Angle     :  0.477   7.748  20146  Z= 0.259
  Chirality :  0.037   0.139   2305
  Planarity :  0.003   0.026   2070
  Dihedral  : 16.164  98.833   6242
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  6.21 %
    Favored  : 91.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.23), residues: 1339
  helix:  1.51 (0.20), residues: 691
  sheet: -0.59 (0.46), residues: 130
  loop : -0.10 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 476 
 HIS   0.003   0.001   HIS B 328 
 PHE   0.010   0.001   PHE B1204 
 TYR   0.009   0.001   TYR B 155 
 ARG   0.003   0.000   ARG B 925 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11265 (  651)
  hydrogen bonds       : angle       5.01801 ( 1786)
  covalent geometry    : bond        0.00465 (14481)
  covalent geometry    : angle       0.47654 (20146)

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

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

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 76
  time to evaluate  : 1.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  216 LEU cc_start: 0.9174 (mt) cc_final: 0.8937 (mp)
REVERT: B  248 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5375 (tm)
REVERT: B  879 MET cc_start: 0.8413 (mmm) cc_final: 0.7928 (mmm)
REVERT: B 1078 ARG cc_start: 0.8304 (ptp-110) cc_final: 0.7776 (ptm-80)
  outliers start: 26
  outliers final: 4
  residues processed: 101
  average time/residue: 2.0941
  time to fit residues: 232.5109
Evaluate side-chains
  36 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 1.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 ASN
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  627 GLU
Chi-restraints excluded: chain B residue 1033 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    4.9990
   chunk 110 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 37 optimal weight:   20.0000
   chunk 74 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 114 optimal weight:    6.9990
   chunk 44 optimal weight:    7.9990
   chunk 69 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 132 optimal weight:    0.0170
   overall best weight:    0.7218

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

Flipped N/Q/H residues before XYZ refinement:
B 113 HIS
** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 544 GLN
B 588 ASN
B 650 GLN
B 668 ASN
B 695 GLN
B 805 GLN
B 826 GLN
B 844 GLN
B 885 GLN
B1262 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.072927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.051711 restraints weight = 39384.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 2.82
r_work: 0.2796 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  14481  Z= 0.109
  Angle     :  0.465   6.730  20146  Z= 0.248
  Chirality :  0.035   0.139   2305
  Planarity :  0.003   0.034   2070
  Dihedral  : 17.974  96.134   3392
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 10.10 %
    Favored  : 88.74 %
  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:  1.21 (0.23), residues: 1339
  helix:  1.79 (0.20), residues: 695
  sheet: -0.73 (0.46), residues: 119
  loop : -0.08 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 476 
 HIS   0.004   0.001   HIS B1297 
 PHE   0.022   0.001   PHE B 290 
 TYR   0.010   0.001   TYR B 155 
 ARG   0.010   0.000   ARG B 535 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04007 (  651)
  hydrogen bonds       : angle       4.03996 ( 1786)
  covalent geometry    : bond        0.00230 (14481)
  covalent geometry    : angle       0.46450 (20146)

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

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

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 1.259 
Fit side-chains
REVERT: B  220 ARG cc_start: 0.8815 (mmm-85) cc_final: 0.8530 (tpp-160)
REVERT: B  248 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5566 (tm)
REVERT: B  534 MET cc_start: 0.8107 (mtp) cc_final: 0.7793 (mtm)
REVERT: B  879 MET cc_start: 0.8349 (mmm) cc_final: 0.7899 (mmm)
REVERT: B 1078 ARG cc_start: 0.8436 (ptp-110) cc_final: 0.7871 (ptm-80)
REVERT: B 1189 GLU cc_start: 0.8239 (mp0) cc_final: 0.7972 (pm20)
  outliers start: 14
  outliers final: 3
  residues processed: 51
  average time/residue: 1.5088
  time to fit residues: 84.7045
Evaluate side-chains
  35 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 1.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  535 ARG
Chi-restraints excluded: chain B residue  627 GLU
Chi-restraints excluded: chain B residue 1240 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 96 optimal weight:    0.1980
   chunk 121 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 133 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 117 optimal weight:    8.9990
   chunk 31 optimal weight:    0.0370
   chunk 19 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    1.2464

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

Flipped N/Q/H residues before XYZ refinement:
B  14 ASN
** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 420 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.072582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.051493 restraints weight = 39648.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 2.82
r_work: 0.2784 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14481  Z= 0.120
  Angle     :  0.444   7.274  20146  Z= 0.237
  Chirality :  0.035   0.145   2305
  Planarity :  0.003   0.037   2070
  Dihedral  : 17.851  99.219   3387
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 10.35 %
    Favored  : 88.00 %
  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:  1.22 (0.23), residues: 1339
  helix:  1.83 (0.20), residues: 689
  sheet: -0.70 (0.46), residues: 119
  loop : -0.10 (0.26), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 476 
 HIS   0.004   0.001   HIS B 328 
 PHE   0.026   0.001   PHE B 290 
 TYR   0.024   0.001   TYR B1013 
 ARG   0.006   0.000   ARG B 653 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03816 (  651)
  hydrogen bonds       : angle       3.85249 ( 1786)
  covalent geometry    : bond        0.00261 (14481)
  covalent geometry    : angle       0.44435 (20146)

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

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

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 34
  time to evaluate  : 1.383 
Fit side-chains
REVERT: B  216 LEU cc_start: 0.9064 (mp) cc_final: 0.8544 (pt)
REVERT: B  248 LEU cc_start: 0.5905 (OUTLIER) cc_final: 0.5661 (tm)
REVERT: B  534 MET cc_start: 0.8080 (mtp) cc_final: 0.7789 (mtm)
REVERT: B  879 MET cc_start: 0.8484 (mmm) cc_final: 0.8029 (mmm)
REVERT: B 1296 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8823 (tmtt)
  outliers start: 20
  outliers final: 9
  residues processed: 52
  average time/residue: 1.1857
  time to fit residues: 69.4169
Evaluate side-chains
  42 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  535 ARG
Chi-restraints excluded: chain B residue  616 LEU
Chi-restraints excluded: chain B residue  627 GLU
Chi-restraints excluded: chain B residue 1033 THR
Chi-restraints excluded: chain B residue 1164 LEU
Chi-restraints excluded: chain B residue 1216 SER
Chi-restraints excluded: chain B residue 1240 SER
Chi-restraints excluded: chain B residue 1296 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 134 optimal weight:   20.0000
   chunk 117 optimal weight:    8.9990
   chunk 57 optimal weight:    4.9990
   chunk 133 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 145 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 127 optimal weight:    0.9990
   chunk 131 optimal weight:    6.9990
   chunk 125 optimal weight:    9.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
B 930 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.070929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.049593 restraints weight = 39535.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 2.82
r_work: 0.2734 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  14481  Z= 0.195
  Angle     :  0.480   6.840  20146  Z= 0.256
  Chirality :  0.037   0.135   2305
  Planarity :  0.003   0.040   2070
  Dihedral  : 17.901  99.704   3387
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 10.84 %
    Favored  : 87.33 %
  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:  1.17 (0.23), residues: 1339
  helix:  1.78 (0.20), residues: 689
  sheet: -0.77 (0.46), residues: 119
  loop : -0.10 (0.26), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 476 
 HIS   0.004   0.001   HIS B 328 
 PHE   0.013   0.001   PHE B1204 
 TYR   0.024   0.001   TYR B1013 
 ARG   0.009   0.000   ARG B1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04221 (  651)
  hydrogen bonds       : angle       3.93837 ( 1786)
  covalent geometry    : bond        0.00437 (14481)
  covalent geometry    : angle       0.48040 (20146)

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

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

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 33
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
REVERT: B  216 LEU cc_start: 0.9049 (mp) cc_final: 0.8828 (pp)
REVERT: B  248 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5630 (tm)
REVERT: B  534 MET cc_start: 0.8100 (mtp) cc_final: 0.7763 (mtm)
REVERT: B  879 MET cc_start: 0.8636 (mmm) cc_final: 0.8097 (mmm)
REVERT: B 1189 GLU cc_start: 0.8336 (mp0) cc_final: 0.8087 (pm20)
REVERT: B 1242 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.7381 (m-80)
REVERT: B 1296 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8838 (tmtt)
  outliers start: 22
  outliers final: 10
  residues processed: 52
  average time/residue: 1.2949
  time to fit residues: 75.2501
Evaluate side-chains
  45 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LYS
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  535 ARG
Chi-restraints excluded: chain B residue  616 LEU
Chi-restraints excluded: chain B residue  627 GLU
Chi-restraints excluded: chain B residue 1033 THR
Chi-restraints excluded: chain B residue 1146 VAL
Chi-restraints excluded: chain B residue 1164 LEU
Chi-restraints excluded: chain B residue 1216 SER
Chi-restraints excluded: chain B residue 1240 SER
Chi-restraints excluded: chain B residue 1242 TYR
Chi-restraints excluded: chain B residue 1296 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 83 optimal weight:    0.1980
   chunk 5 optimal weight:    7.9990
   chunk 98 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 113 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 89 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1297 HIS ** 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 = 0.3414 r_free = 0.3414 target = 0.072815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.051832 restraints weight = 39774.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 2.80
r_work: 0.2795 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  14481  Z= 0.105
  Angle     :  0.427   6.990  20146  Z= 0.229
  Chirality :  0.034   0.146   2305
  Planarity :  0.003   0.039   2070
  Dihedral  : 17.826  99.366   3387
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.75 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.23), residues: 1339
  helix:  1.88 (0.20), residues: 688
  sheet: -0.49 (0.49), residues: 109
  loop : -0.14 (0.26), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 476 
 HIS   0.003   0.001   HIS B 328 
 PHE   0.008   0.001   PHE B1045 
 TYR   0.024   0.001   TYR B1013 
 ARG   0.006   0.000   ARG B1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03684 (  651)
  hydrogen bonds       : angle       3.75027 ( 1786)
  covalent geometry    : bond        0.00228 (14481)
  covalent geometry    : angle       0.42714 (20146)

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

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

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 33
  time to evaluate  : 1.301 
Fit side-chains
   revert: symmetry clash
REVERT: B  216 LEU cc_start: 0.9040 (mp) cc_final: 0.8093 (pp)
REVERT: B  220 ARG cc_start: 0.8755 (mmm-85) cc_final: 0.8497 (tmm-80)
REVERT: B  248 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5736 (tm)
REVERT: B  534 MET cc_start: 0.8094 (mtp) cc_final: 0.7732 (mtm)
REVERT: B  879 MET cc_start: 0.8579 (mmm) cc_final: 0.8031 (mmm)
REVERT: B 1242 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7257 (m-80)
REVERT: B 1296 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8850 (tmtt)
  outliers start: 20
  outliers final: 8
  residues processed: 51
  average time/residue: 1.3360
  time to fit residues: 76.2162
Evaluate side-chains
  42 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 1.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 LYS
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  535 ARG
Chi-restraints excluded: chain B residue  627 GLU
Chi-restraints excluded: chain B residue  801 VAL
Chi-restraints excluded: chain B residue 1033 THR
Chi-restraints excluded: chain B residue 1164 LEU
Chi-restraints excluded: chain B residue 1216 SER
Chi-restraints excluded: chain B residue 1240 SER
Chi-restraints excluded: chain B residue 1242 TYR
Chi-restraints excluded: chain B residue 1296 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 38 optimal weight:   30.0000
   chunk 71 optimal weight:    6.9990
   chunk 106 optimal weight:    6.9990
   chunk 79 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 36 optimal weight:   20.0000
   chunk 7 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 133 optimal weight:    0.9980
   chunk 12 optimal weight:    7.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1297 HIS ** 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 = 0.3340 r_free = 0.3340 target = 0.069467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.048040 restraints weight = 40356.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 2.84
r_work: 0.2694 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038  14481  Z= 0.307
  Angle     :  0.557   7.000  20146  Z= 0.294
  Chirality :  0.040   0.140   2305
  Planarity :  0.003   0.042   2070
  Dihedral  : 17.967 100.442   3387
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.84 %
    Favored  : 86.01 %
  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:  1.00 (0.23), residues: 1339
  helix:  1.63 (0.20), residues: 695
  sheet: -0.92 (0.47), residues: 117
  loop : -0.17 (0.27), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 476 
 HIS   0.004   0.001   HIS B 328 
 PHE   0.017   0.001   PHE B1204 
 TYR   0.025   0.002   TYR B1013 
 ARG   0.006   0.001   ARG B1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04769 (  651)
  hydrogen bonds       : angle       4.10198 ( 1786)
  covalent geometry    : bond        0.00690 (14481)
  covalent geometry    : angle       0.55662 (20146)

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

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

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 34
  time to evaluate  : 1.453 
Fit side-chains
   revert: symmetry clash
REVERT: B  221 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6345 (ptt180)
REVERT: B  246 LEU cc_start: 0.6851 (pp) cc_final: 0.6559 (pp)
REVERT: B  534 MET cc_start: 0.8154 (mtp) cc_final: 0.7747 (mtm)
REVERT: B  535 ARG cc_start: 0.7638 (tpm170) cc_final: 0.7421 (OUTLIER)
REVERT: B 1042 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8675 (tp)
REVERT: B 1242 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7589 (m-80)
REVERT: B 1296 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8872 (tmtt)
REVERT: B 1333 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8161 (ptt-90)
  outliers start: 26
  outliers final: 11
  residues processed: 55
  average time/residue: 1.2174
  time to fit residues: 75.2333
Evaluate side-chains
  46 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 31
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue  221 ARG
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  627 GLU
Chi-restraints excluded: chain B residue  657 THR
Chi-restraints excluded: chain B residue  801 VAL
Chi-restraints excluded: chain B residue 1033 THR
Chi-restraints excluded: chain B residue 1042 ILE
Chi-restraints excluded: chain B residue 1146 VAL
Chi-restraints excluded: chain B residue 1164 LEU
Chi-restraints excluded: chain B residue 1216 SER
Chi-restraints excluded: chain B residue 1240 SER
Chi-restraints excluded: chain B residue 1242 TYR
Chi-restraints excluded: chain B residue 1296 LYS
Chi-restraints excluded: chain B residue 1333 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 124 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   chunk 138 optimal weight:    3.9990
   chunk 139 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 115 optimal weight:    0.0970
   chunk 18 optimal weight:    0.9990
   chunk 36 optimal weight:   20.0000
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
B 224 ASN
** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.071946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.050863 restraints weight = 39925.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 2.79
r_work: 0.2770 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14481  Z= 0.116
  Angle     :  0.445   6.705  20146  Z= 0.239
  Chirality :  0.035   0.152   2305
  Planarity :  0.003   0.037   2070
  Dihedral  : 17.808  99.608   3385
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.83 %
    Favored  : 85.76 %
  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:  1.23 (0.23), residues: 1339
  helix:  1.85 (0.20), residues: 687
  sheet: -0.59 (0.50), residues: 109
  loop : -0.16 (0.27), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 476 
 HIS   0.003   0.001   HIS B 328 
 PHE   0.007   0.001   PHE B1045 
 TYR   0.025   0.001   TYR B1013 
 ARG   0.005   0.000   ARG B1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03802 (  651)
  hydrogen bonds       : angle       3.82139 ( 1786)
  covalent geometry    : bond        0.00252 (14481)
  covalent geometry    : angle       0.44473 (20146)

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

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

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 31
  time to evaluate  : 1.324 
Fit side-chains
   revert: symmetry clash
REVERT: B  534 MET cc_start: 0.8091 (mtp) cc_final: 0.7722 (mtm)
REVERT: B  535 ARG cc_start: 0.7666 (tpm170) cc_final: 0.7465 (OUTLIER)
REVERT: B  628 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6524 (p0)
REVERT: B 1242 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.7280 (m-80)
REVERT: B 1296 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8870 (tmtt)
  outliers start: 17
  outliers final: 9
  residues processed: 45
  average time/residue: 1.4225
  time to fit residues: 71.2143
Evaluate side-chains
  41 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 30
  time to evaluate  : 1.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  627 GLU
Chi-restraints excluded: chain B residue  628 ASP
Chi-restraints excluded: chain B residue  801 VAL
Chi-restraints excluded: chain B residue 1033 THR
Chi-restraints excluded: chain B residue 1146 VAL
Chi-restraints excluded: chain B residue 1164 LEU
Chi-restraints excluded: chain B residue 1216 SER
Chi-restraints excluded: chain B residue 1240 SER
Chi-restraints excluded: chain B residue 1242 TYR
Chi-restraints excluded: chain B residue 1296 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 127 optimal weight:    0.4980
   chunk 143 optimal weight:    0.0770
   chunk 97 optimal weight:    1.9990
   chunk 133 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 142 optimal weight:    0.2980
   chunk 30 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1297 HIS ** 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 = 0.3433 r_free = 0.3433 target = 0.073744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.052813 restraints weight = 39200.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 2.82
r_work: 0.2824 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  14481  Z= 0.091
  Angle     :  0.426   9.752  20146  Z= 0.227
  Chirality :  0.034   0.208   2305
  Planarity :  0.003   0.034   2070
  Dihedral  : 17.670  99.358   3385
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.83 %
    Favored  : 85.84 %
  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:  1.37 (0.23), residues: 1339
  helix:  2.00 (0.20), residues: 688
  sheet: -0.55 (0.51), residues: 108
  loop : -0.14 (0.26), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B1074 
 HIS   0.003   0.001   HIS B 328 
 PHE   0.007   0.001   PHE B1045 
 TYR   0.031   0.001   TYR B1013 
 ARG   0.005   0.000   ARG B1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03457 (  651)
  hydrogen bonds       : angle       3.62095 ( 1786)
  covalent geometry    : bond        0.00191 (14481)
  covalent geometry    : angle       0.42602 (20146)

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

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

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 32
  time to evaluate  : 1.304 
Fit side-chains
   revert: symmetry clash
REVERT: B  183 LYS cc_start: 0.8757 (mmtm) cc_final: 0.8556 (tptt)
REVERT: B  534 MET cc_start: 0.8132 (mtp) cc_final: 0.7770 (mtm)
REVERT: B  628 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.6445 (p0)
REVERT: B  879 MET cc_start: 0.8523 (mmm) cc_final: 0.8065 (mmm)
REVERT: B 1242 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7158 (m-80)
REVERT: B 1296 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8930 (tttt)
  outliers start: 16
  outliers final: 7
  residues processed: 46
  average time/residue: 1.4913
  time to fit residues: 76.0772
Evaluate side-chains
  40 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  535 ARG
Chi-restraints excluded: chain B residue  627 GLU
Chi-restraints excluded: chain B residue  628 ASP
Chi-restraints excluded: chain B residue  801 VAL
Chi-restraints excluded: chain B residue 1033 THR
Chi-restraints excluded: chain B residue 1146 VAL
Chi-restraints excluded: chain B residue 1164 LEU
Chi-restraints excluded: chain B residue 1242 TYR
Chi-restraints excluded: chain B residue 1296 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 135 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 65 optimal weight:    0.3980
   chunk 75 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 129 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1297 HIS ** 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 = 0.3423 r_free = 0.3423 target = 0.073267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.052391 restraints weight = 39641.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 2.76
r_work: 0.2809 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  14481  Z= 0.106
  Angle     :  0.426   7.397  20146  Z= 0.228
  Chirality :  0.034   0.163   2305
  Planarity :  0.003   0.037   2070
  Dihedral  : 17.661  98.818   3385
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.16 %
    Favored  : 85.84 %
  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:  1.42 (0.23), residues: 1339
  helix:  2.02 (0.20), residues: 686
  sheet: -0.44 (0.51), residues: 110
  loop : -0.10 (0.27), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 464 
 HIS   0.003   0.001   HIS B 328 
 PHE   0.007   0.001   PHE B1204 
 TYR   0.028   0.001   TYR B1013 
 ARG   0.005   0.000   ARG B1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03589 (  651)
  hydrogen bonds       : angle       3.62812 ( 1786)
  covalent geometry    : bond        0.00229 (14481)
  covalent geometry    : angle       0.42637 (20146)

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

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

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 31
  time to evaluate  : 1.384 
Fit side-chains
REVERT: B  534 MET cc_start: 0.8183 (mtp) cc_final: 0.7842 (mtm)
REVERT: B  535 ARG cc_start: 0.7668 (tpm170) cc_final: 0.7395 (OUTLIER)
REVERT: B  628 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6925 (p0)
REVERT: B 1242 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7145 (m-80)
REVERT: B 1296 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8971 (tttt)
  outliers start: 12
  outliers final: 6
  residues processed: 42
  average time/residue: 1.4736
  time to fit residues: 68.9281
Evaluate side-chains
  36 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  627 GLU
Chi-restraints excluded: chain B residue  628 ASP
Chi-restraints excluded: chain B residue  801 VAL
Chi-restraints excluded: chain B residue 1033 THR
Chi-restraints excluded: chain B residue 1164 LEU
Chi-restraints excluded: chain B residue 1240 SER
Chi-restraints excluded: chain B residue 1242 TYR
Chi-restraints excluded: chain B residue 1296 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 113 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 139 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 125 optimal weight:    8.9990
   chunk 78 optimal weight:    0.8980
   chunk 135 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1297 HIS ** 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 = 0.3428 r_free = 0.3428 target = 0.073548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.052675 restraints weight = 39643.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 2.77
r_work: 0.2818 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  14481  Z= 0.101
  Angle     :  0.425   6.770  20146  Z= 0.228
  Chirality :  0.034   0.164   2305
  Planarity :  0.003   0.051   2070
  Dihedral  : 17.630  98.371   3385
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 13.25 %
    Favored  : 85.68 %
  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:  1.47 (0.23), residues: 1339
  helix:  2.02 (0.20), residues: 686
  sheet: -0.07 (0.57), residues: 93
  loop : -0.10 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 476 
 HIS   0.003   0.001   HIS B 328 
 PHE   0.007   0.001   PHE B1045 
 TYR   0.025   0.001   TYR B1013 
 ARG   0.010   0.000   ARG B 629 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  651)
  hydrogen bonds       : angle       3.61167 ( 1786)
  covalent geometry    : bond        0.00219 (14481)
  covalent geometry    : angle       0.42509 (20146)

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

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

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2678 Ramachandran restraints generated.
    1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 30
  time to evaluate  : 1.311 
Fit side-chains
REVERT: B  220 ARG cc_start: 0.8645 (mmm-85) cc_final: 0.8349 (tmm-80)
REVERT: B  534 MET cc_start: 0.8271 (mtp) cc_final: 0.7957 (mtm)
REVERT: B  535 ARG cc_start: 0.7717 (tpm170) cc_final: 0.7466 (tpm170)
REVERT: B 1242 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7060 (m-80)
REVERT: B 1296 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8975 (tttt)
  outliers start: 13
  outliers final: 5
  residues processed: 41
  average time/residue: 1.4014
  time to fit residues: 64.0220
Evaluate side-chains
  36 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 1.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  627 GLU
Chi-restraints excluded: chain B residue  801 VAL
Chi-restraints excluded: chain B residue 1033 THR
Chi-restraints excluded: chain B residue 1164 LEU
Chi-restraints excluded: chain B residue 1240 SER
Chi-restraints excluded: chain B residue 1242 TYR
Chi-restraints excluded: chain B residue 1296 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 134 optimal weight:    0.0970
   chunk 73 optimal weight:    0.9990
   chunk 119 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 64 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1297 HIS ** 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 = 0.3400 r_free = 0.3400 target = 0.071989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.050948 restraints weight = 39905.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 2.84
r_work: 0.2783 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14481  Z= 0.134
  Angle     :  0.442   6.341  20146  Z= 0.236
  Chirality :  0.035   0.163   2305
  Planarity :  0.003   0.038   2070
  Dihedral  : 17.670  98.158   3385
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 13.58 %
    Favored  : 85.60 %
  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:  1.41 (0.23), residues: 1339
  helix:  2.00 (0.20), residues: 686
  sheet: -0.41 (0.54), residues: 100
  loop : -0.10 (0.26), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 464 
 HIS   0.004   0.001   HIS B 983 
 PHE   0.010   0.001   PHE B1204 
 TYR   0.026   0.001   TYR B1013 
 ARG   0.005   0.000   ARG B1298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03779 (  651)
  hydrogen bonds       : angle       3.69728 ( 1786)
  covalent geometry    : bond        0.00296 (14481)
  covalent geometry    : angle       0.44207 (20146)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7120.27 seconds
wall clock time: 123 minutes 55.65 seconds (7435.65 seconds total)