Starting phenix.real_space_refine
on Wed Sep 17 23:05:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nl2_49515/09_2025/9nl2_49515.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nl2_49515/09_2025/9nl2_49515.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nl2_49515/09_2025/9nl2_49515.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nl2_49515/09_2025/9nl2_49515.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nl2_49515/09_2025/9nl2_49515.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nl2_49515/09_2025/9nl2_49515.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 121 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Zn      4      6.06       5
     P     159      5.49       5
     Mg      1      5.21       5
     S      50      5.16       5
     C    7134      2.51       5
     N    2172      2.21       5
     O    2618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12138
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 8854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1107, 8854
          Classifications: {'peptide': 1107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1049}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 791
          Classifications: {'DNA': 39}
          Link IDs: {'rna3p': 38}
    Chain: "P"
      Number of atoms: 267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 267
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 1140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 1140
          Classifications: {'RNA': 53}
          Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p_pur': 24, 'rna3p_pyr': 18}
          Link IDs: {'rna2p': 11, 'rna3p': 41}
          Chain breaks: 2
    Chain: "T"
      Number of atoms: 1052
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 1052
          Classifications: {'DNA': 51}
          Link IDs: {'rna3p': 50}
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 34
          Unusual residues: {' MG': 1, ' ZN': 4, 'TTP': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    107  SG  CYS A  14      79.077  95.346  69.639  1.00 95.68           S
  ATOM    131  SG  CYS A  17      82.012  97.787  70.031  1.00101.52           S
  ATOM    340  SG  CYS A  44      60.507  92.311  61.054  1.00 92.73           S
  ATOM    360  SG  CYS A  47      57.484  89.668  62.141  1.00101.78           S
  ATOM    489  SG  CYS A  64      57.087  92.335  59.338  1.00 99.79           S
  ATOM    594  SG  CYS A  78      47.731  69.980  70.976  1.00 86.36           S
  ATOM    616  SG  CYS A  81      50.695  72.437  70.309  1.00 87.31           S
  ATOM   7380  SG  CYS A 941      93.349 100.820  36.648  1.00 91.42           S
  ATOM   7405  SG  CYS A 944      95.312 102.733  33.786  1.00 83.84           S
  ATOM   7509  SG  CYS A 958      96.971 100.002  35.868  1.00 91.83           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C1' TTP A1206 " occ=0.65
      ... (27 atoms not shown)
      pdb=" PG  TTP A1206 " occ=0.65
  Time building chain proxies: 3.36, per 1000 atoms: 0.28
  Number of scatterers: 12138
  At special positions: 0
  Unit cell: (133.096, 119.472, 100.608, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      4     29.99
     S      50     16.00
     P     159     15.00
     Mg      1     11.99
     O    2618      8.00
     N    2172      7.00
     C    7134      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.21
  Conformation dependent library (CDL) restraints added in 563.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1202 "
        pdb="ZN    ZN A1202 " - pdb=" NE2 HIS A  35 "
        pdb="ZN    ZN A1202 " - pdb=" NE2 HIS A  30 "
        pdb="ZN    ZN A1202 " - pdb=" SG  CYS A  17 "
        pdb="ZN    ZN A1202 " - pdb=" SG  CYS A  14 "
      pdb="  ZN A1203 "
        pdb="ZN    ZN A1203 " - pdb=" NE2 HIS A  60 "
        pdb="ZN    ZN A1203 " - pdb=" SG  CYS A  64 "
        pdb="ZN    ZN A1203 " - pdb=" SG  CYS A  44 "
        pdb="ZN    ZN A1203 " - pdb=" SG  CYS A  47 "
      pdb="  ZN A1204 "
        pdb="ZN    ZN A1204 " - pdb=" NE2 HIS A  99 "
        pdb="ZN    ZN A1204 " - pdb=" NE2 HIS A  94 "
        pdb="ZN    ZN A1204 " - pdb=" SG  CYS A  81 "
        pdb="ZN    ZN A1204 " - pdb=" SG  CYS A  78 "
      pdb="  ZN A1205 "
        pdb="ZN    ZN A1205 " - pdb=" NE2 HIS A 953 "
        pdb="ZN    ZN A1205 " - pdb=" SG  CYS A 958 "
        pdb="ZN    ZN A1205 " - pdb=" SG  CYS A 941 "
        pdb="ZN    ZN A1205 " - pdb=" SG  CYS A 944 "
      Number of angles added : 10


  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 10 sheets defined
      55.0% alpha, 5.7% beta
      55 base pairs and 100 stacking pairs defined.
    Time for finding SS restraints: 2.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 35
    Processing helix  chain 'A' and resid 53 through 64
      removed outlier: 3.737A  pdb=" N   ILE A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      Proline residue:  A  62  - end of helix
    Processing helix  chain 'A' and resid 87 through 99
    Processing helix  chain 'A' and resid 99 through 112
    Processing helix  chain 'A' and resid 127 through 141
    Processing helix  chain 'A' and resid 149 through 155
      removed outlier: 4.226A  pdb=" N   ASP A 153 " --> pdb=" O   ILE A 149 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ILE A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 170
    Processing helix  chain 'A' and resid 203 through 220
      removed outlier: 3.628A  pdb=" N   THR A 208 " --> pdb=" O   GLY A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
    Processing helix  chain 'A' and resid 239 through 256
    Processing helix  chain 'A' and resid 284 through 301
    Processing helix  chain 'A' and resid 303 through 313
    Processing helix  chain 'A' and resid 322 through 335
    Processing helix  chain 'A' and resid 353 through 358
      removed outlier: 3.563A  pdb=" N   ALA A 356 " --> pdb=" O   ASP A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 372
    Processing helix  chain 'A' and resid 385 through 393
    Processing helix  chain 'A' and resid 396 through 410
    Processing helix  chain 'A' and resid 413 through 417
    Processing helix  chain 'A' and resid 429 through 435
      removed outlier: 4.211A  pdb=" N   GLU A 435 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 464
    Processing helix  chain 'A' and resid 477 through 497
      removed outlier: 3.736A  pdb=" N   GLU A 481 " --> pdb=" O   PRO A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 524
    Processing helix  chain 'A' and resid 529 through 540
    Processing helix  chain 'A' and resid 568 through 588
      removed outlier: 4.600A  pdb=" N   LEU A 572 " --> pdb=" O   PRO A 568 " (cutoff:3.500A)
      Proline residue:  A 580  - end of helix
    Processing helix  chain 'A' and resid 614 through 633
    Processing helix  chain 'A' and resid 662 through 666
    Processing helix  chain 'A' and resid 694 through 708
    Processing helix  chain 'A' and resid 712 through 724
    Processing helix  chain 'A' and resid 724 through 735
      removed outlier: 3.737A  pdb=" N   ILE A 728 " --> pdb=" O   THR A 724 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   LEU A 731 " --> pdb=" O   ARG A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 758
    Processing helix  chain 'A' and resid 764 through 770
      removed outlier: 3.575A  pdb=" N   ILE A 768 " --> pdb=" O   CYS A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 775
    Processing helix  chain 'A' and resid 781 through 799
      Proline residue:  A 787  - end of helix
    Processing helix  chain 'A' and resid 802 through 812
      removed outlier: 3.618A  pdb=" N   ASN A 812 " --> pdb=" O   ILE A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 825
      removed outlier: 3.751A  pdb=" N   GLU A 817 " --> pdb=" O   ASN A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 846 through 853
      removed outlier: 3.581A  pdb=" N   LEU A 853 " --> pdb=" O   ILE A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 870 through 882
      removed outlier: 3.617A  pdb=" N   LEU A 882 " --> pdb=" O   HIS A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 904
      removed outlier: 4.074A  pdb=" N   GLN A 903 " --> pdb=" O   ASN A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 922
    Processing helix  chain 'A' and resid 926 through 931
    Processing helix  chain 'A' and resid 950 through 957
    Processing helix  chain 'A' and resid 958 through 960
      No H-bonds generated for 'chain 'A' and resid 958 through 960'
    Processing helix  chain 'A' and resid 961 through 983
    Processing helix  chain 'A' and resid 1026 through 1038
      removed outlier: 4.546A  pdb=" N   GLU A1030 " --> pdb=" O   GLU A1026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1040 through 1042
      No H-bonds generated for 'chain 'A' and resid 1040 through 1042'
    Processing helix  chain 'A' and resid 1043 through 1052
    Processing helix  chain 'A' and resid 1070 through 1081
      removed outlier: 3.940A  pdb=" N   GLU A1074 " --> pdb=" O   PRO A1070 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1083 through 1120
      removed outlier: 4.984A  pdb=" N   GLY A1113 " --> pdb=" O   PHE A1109 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LYS A1114 " --> pdb=" O   GLU A1110 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   ASN A1116 " --> pdb=" O   ILE A1112 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77
    Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 425
    Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 604
      removed outlier: 3.519A  pdb=" N   GLY A 643 " --> pdb=" O   ASN A 669 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 507 through 508
      removed outlier: 4.479A  pdb=" N   LYS A 635 " --> pdb=" O   ALA A 508 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 548 through 549
    Processing sheet with id=AA7, first strand: chain 'A' and resid 684 through 685
    Processing sheet with id=AA8, first strand: chain 'A' and resid 841 through 842
    Processing sheet with id=AA9, first strand: chain 'A' and resid 986 through 989
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1018 through 1021
      removed outlier: 6.450A  pdb=" N   THR A1019 " --> pdb=" O   LEU A1063 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    438 hydrogen bonds defined for protein.
    1263 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      139 hydrogen bonds
      270 hydrogen bond angles
      0 basepair planarities
      55 basepair parallelities
      100 stacking parallelities
  Total time for adding SS restraints: 3.83

  Time building geometry restraints manager: 1.58 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: 2628
        1.33 -     1.45: 3408
        1.45 -     1.57: 6290
        1.57 -     1.70: 311
        1.70 -     1.82: 73
  Bond restraints: 12710
  Sorted by residual:
  bond pdb=" N   GLN A   1 "
       pdb=" CA  GLN A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.03e+00
  bond pdb=" CB  MET A 157 "
       pdb=" CG  MET A 157 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.34e+00
  bond pdb=" C1'  DC B  24 "
       pdb=" N1   DC B  24 "
    ideal  model  delta    sigma   weight residual
    1.490  1.536 -0.046 3.00e-02 1.11e+03 2.33e+00
  bond pdb=" N1   DC B  61 "
       pdb=" C2   DC B  61 "
    ideal  model  delta    sigma   weight residual
    1.399  1.370  0.029 2.00e-02 2.50e+03 2.17e+00
  bond pdb=" C1'  DC T  11 "
       pdb=" N1   DC T  11 "
    ideal  model  delta    sigma   weight residual
    1.490  1.533 -0.043 3.00e-02 1.11e+03 2.04e+00
  ... (remaining 12705 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.30: 17878
        8.30 -    16.61: 2
       16.61 -    24.91: 2
       24.91 -    33.22: 4
       33.22 -    41.52: 1
  Bond angle restraints: 17887
  Sorted by residual:
  angle pdb=" OP1  DC B  57 "
        pdb=" P    DC B  57 "
        pdb=" OP2  DC B  57 "
      ideal   model   delta    sigma   weight residual
     120.00   78.48   41.52 3.00e+00 1.11e-01 1.92e+02
  angle pdb=" O3'  DA B  56 "
        pdb=" P    DC B  57 "
        pdb=" OP1  DC B  57 "
      ideal   model   delta    sigma   weight residual
     108.00   76.01   31.99 3.00e+00 1.11e-01 1.14e+02
  angle pdb=" OP2  DC B  57 "
        pdb=" P    DC B  57 "
        pdb=" O5'  DC B  57 "
      ideal   model   delta    sigma   weight residual
     108.00   76.63   31.37 3.00e+00 1.11e-01 1.09e+02
  angle pdb=" O3'  DA B  56 "
        pdb=" P    DC B  57 "
        pdb=" OP2  DC B  57 "
      ideal   model   delta    sigma   weight residual
     108.00  139.35  -31.35 3.00e+00 1.11e-01 1.09e+02
  angle pdb=" O3'  DA B  28 "
        pdb=" P    DA B  29 "
        pdb=" OP1  DA B  29 "
      ideal   model   delta    sigma   weight residual
     108.00   80.96   27.04 3.00e+00 1.11e-01 8.13e+01
  ... (remaining 17882 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.71: 6678
       33.71 -    67.41: 770
       67.41 -   101.12: 40
      101.12 -   134.83: 3
      134.83 -   168.54: 6
  Dihedral angle restraints: 7497
    sinusoidal: 4269
      harmonic: 3228
  Sorted by residual:
  dihedral pdb=" O4'   U R 248 "
           pdb=" C1'   U R 248 "
           pdb=" N1    U R 248 "
           pdb=" C2    U R 248 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   76.20  123.80     1      1.50e+01 4.44e-03 6.64e+01
  dihedral pdb=" C2  TTP A1206 "
           pdb=" C1' TTP A1206 "
           pdb=" N1  TTP A1206 "
           pdb=" O4' TTP A1206 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.68  160.15  141.54     1      2.00e+01 2.50e-03 4.28e+01
  dihedral pdb=" CA  PRO A 477 "
           pdb=" C   PRO A 477 "
           pdb=" N   GLY A 478 "
           pdb=" CA  GLY A 478 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.23   23.77     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 7494 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.400: 2041
       0.400 -    0.800: 0
       0.800 -    1.199: 0
       1.199 -    1.599: 0
       1.599 -    1.999: 1
  Chirality restraints: 2042
  Sorted by residual:
  chirality pdb=" P    DA B  29 "
            pdb=" OP1  DA B  29 "
            pdb=" OP2  DA B  29 "
            pdb=" O5'  DA B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    0.35    2.00 2.00e-01 2.50e+01 9.99e+01
  chirality pdb=" CA  PRO A 713 "
            pdb=" N   PRO A 713 "
            pdb=" C   PRO A 713 "
            pdb=" CB  PRO A 713 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.13e-01
  chirality pdb=" CA  ILE A   5 "
            pdb=" N   ILE A   5 "
            pdb=" C   ILE A   5 "
            pdb=" CB  ILE A   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.02e-01
  ... (remaining 2039 not shown)

  Planarity restraints: 1718
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 138 "    0.013 2.00e-02 2.50e+03   2.67e-02 7.11e+00
        pdb=" CG  ASN A 138 "   -0.046 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 138 "    0.017 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 138 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC B  61 "   -0.026 2.00e-02 2.50e+03   1.65e-02 6.15e+00
        pdb=" N1   DC B  61 "    0.025 2.00e-02 2.50e+03
        pdb=" C2   DC B  61 "    0.029 2.00e-02 2.50e+03
        pdb=" O2   DC B  61 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3   DC B  61 "   -0.014 2.00e-02 2.50e+03
        pdb=" C4   DC B  61 "    0.001 2.00e-02 2.50e+03
        pdb=" N4   DC B  61 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5   DC B  61 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DC B  61 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 282 "    0.012 2.00e-02 2.50e+03   2.44e-02 5.94e+00
        pdb=" C   MET A 282 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   MET A 282 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLU A 283 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1715 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.44: 84
        2.44 -     3.06: 8236
        3.06 -     3.67: 20676
        3.67 -     4.29: 30295
        4.29 -     4.90: 46744
  Nonbonded interactions: 106035
  Sorted by model distance:
  nonbonded pdb="MG    MG A1201 "
            pdb=" O1B TTP A1206 "
     model   vdw
     1.829 2.170
  nonbonded pdb=" OG1 THR A 740 "
            pdb=" OP2  DA T  33 "
     model   vdw
     1.901 3.040
  nonbonded pdb=" OG  SER A 593 "
            pdb=" OD2 ASP A 613 "
     model   vdw
     1.907 3.040
  nonbonded pdb=" O   ILE A 251 "
            pdb=" OG1 THR A 254 "
     model   vdw
     1.934 3.040
  nonbonded pdb=" N2   DG B  60 "
            pdb=" O2   DC T  11 "
     model   vdw
     1.984 3.120
  ... (remaining 106030 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=0.65 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:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     18.640
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
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      :  0.004   0.046  12726  Z= 0.170
  Angle     :  0.888  41.522  17897  Z= 0.412
  Chirality :  0.060   1.999   2042
  Planarity :  0.004   0.044   1718
  Dihedral  : 23.572 168.536   5397
  Min Nonbonded Distance : 1.829

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  7.43 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 20.41 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.26), residues: 1103
  helix:  1.52 (0.23), residues: 530
  sheet: -0.92 (0.60), residues: 63
  loop : -1.28 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 934 
 TYR   0.010   0.001   TYR A 330 
 PHE   0.018   0.001   PHE A1059 
 TRP   0.005   0.001   TRP A 615 
 HIS   0.005   0.001   HIS A 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (12710)
  covalent geometry    : angle       0.88212 (17887)
  hydrogen bonds       : bond        0.11330 (  577)
  hydrogen bonds       : angle       6.36050 ( 1533)
  metal coordination   : bond        0.01366 (   16)
  metal coordination   : angle       4.46498 (   10)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: A  400 GLU cc_start: 0.8250 (tt0) cc_final: 0.8045 (tt0)
  outliers start: 3
  outliers final: 3
  residues processed: 100
  average time/residue: 0.1275
  time to fit residues: 18.0295
Evaluate side-chains
  92 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASN
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue  944 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 123 optimal weight:    6.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 154 HIS
A 544 HIS
A 589 ASN
A 894 ASN
A 962 GLN
A 969 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.151573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.111835 restraints weight = 18963.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.97
r_work: 0.3228 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3087
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  12726  Z= 0.264
  Angle     :  0.932  40.369  17897  Z= 0.432
  Chirality :  0.063   2.005   2042
  Planarity :  0.005   0.042   1718
  Dihedral  : 25.620 177.728   3127
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  6.62 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 19.49 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.26), residues: 1103
  helix:  1.60 (0.23), residues: 540
  sheet: -0.94 (0.57), residues: 63
  loop : -1.25 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1038 
 TYR   0.012   0.002   TYR A 924 
 PHE   0.016   0.002   PHE A 644 
 TRP   0.008   0.002   TRP A 871 
 HIS   0.008   0.001   HIS A 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 (12710)
  covalent geometry    : angle       0.92960 (17887)
  hydrogen bonds       : bond        0.05664 (  577)
  hydrogen bonds       : angle       4.95526 ( 1533)
  metal coordination   : bond        0.01198 (   16)
  metal coordination   : angle       2.87074 (   10)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7664 (tpp80) cc_final: 0.6817 (mmm-85)
REVERT: A  281 TRP cc_start: 0.6691 (m100) cc_final: 0.6266 (t-100)
REVERT: A  373 MET cc_start: 0.8932 (mtp) cc_final: 0.8523 (mtp)
REVERT: A  400 GLU cc_start: 0.8464 (tt0) cc_final: 0.8213 (tt0)
REVERT: A  596 LYS cc_start: 0.8223 (mmmt) cc_final: 0.7993 (mtpt)
  outliers start: 27
  outliers final: 19
  residues processed: 117
  average time/residue: 0.1258
  time to fit residues: 20.8016
Evaluate side-chains
  111 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  538 ASP
Chi-restraints excluded: chain A residue  547 MET
Chi-restraints excluded: chain A residue  589 ASN
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  764 CYS
Chi-restraints excluded: chain A residue  784 SER
Chi-restraints excluded: chain A residue  835 ILE
Chi-restraints excluded: chain A residue 1051 THR
Chi-restraints excluded: chain A residue 1078 THR
Chi-restraints excluded: chain A residue 1120 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 74 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 589 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.153235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.113428 restraints weight = 19051.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 1.88
r_work: 0.3237 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3239
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  12726  Z= 0.158
  Angle     :  0.871  40.078  17897  Z= 0.395
  Chirality :  0.059   1.985   2042
  Planarity :  0.004   0.034   1718
  Dihedral  : 25.497 177.283   3124
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  5.89 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.98 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.26), residues: 1103
  helix:  1.72 (0.23), residues: 542
  sheet: -0.86 (0.54), residues: 69
  loop : -1.21 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 834 
 TYR   0.010   0.002   TYR A 723 
 PHE   0.012   0.001   PHE A 908 
 TRP   0.007   0.001   TRP A 985 
 HIS   0.005   0.001   HIS A 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (12710)
  covalent geometry    : angle       0.86989 (17887)
  hydrogen bonds       : bond        0.04846 (  577)
  hydrogen bonds       : angle       4.73808 ( 1533)
  metal coordination   : bond        0.00725 (   16)
  metal coordination   : angle       2.34089 (   10)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 106
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7387 (tpp80) cc_final: 0.6588 (mmm-85)
REVERT: A  281 TRP cc_start: 0.6510 (m100) cc_final: 0.6162 (t-100)
REVERT: A  358 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7750 (mp0)
REVERT: A  373 MET cc_start: 0.8759 (mtp) cc_final: 0.8211 (mtp)
REVERT: A  400 GLU cc_start: 0.8275 (tt0) cc_final: 0.7997 (tt0)
REVERT: A  596 LYS cc_start: 0.8291 (mmmt) cc_final: 0.8015 (mtpt)
REVERT: A  607 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7343 (m-30)
REVERT: A  697 GLU cc_start: 0.8543 (mp0) cc_final: 0.8311 (mp0)
REVERT: A  834 ARG cc_start: 0.8439 (mtp85) cc_final: 0.7764 (mtm-85)
REVERT: A 1038 ARG cc_start: 0.7336 (mtp-110) cc_final: 0.7018 (mtm-85)
REVERT: A 1049 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6471 (mt-10)
REVERT: A 1059 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7762 (p90)
  outliers start: 30
  outliers final: 14
  residues processed: 125
  average time/residue: 0.1170
  time to fit residues: 20.7711
Evaluate side-chains
  115 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  358 GLU
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain A residue  538 ASP
Chi-restraints excluded: chain A residue  589 ASN
Chi-restraints excluded: chain A residue  607 ASP
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  784 SER
Chi-restraints excluded: chain A residue  835 ILE
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue 1059 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 78 optimal weight:    3.9990
   chunk 54 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 116 optimal weight:    6.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 589 ASN
A 878 HIS
A 903 GLN
A 957 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.147573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.106438 restraints weight = 18977.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.20
r_work: 0.3138 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2999
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2999
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.065  12726  Z= 0.348
  Angle     :  0.965  40.139  17897  Z= 0.448
  Chirality :  0.064   1.983   2042
  Planarity :  0.006   0.045   1718
  Dihedral  : 25.653 177.423   3123
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  6.98 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 18.38 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.25), residues: 1103
  helix:  1.36 (0.22), residues: 540
  sheet: -0.99 (0.51), residues: 77
  loop : -1.41 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 440 
 TYR   0.014   0.003   TYR A 924 
 PHE   0.016   0.002   PHE A 644 
 TRP   0.008   0.002   TRP A 985 
 HIS   0.008   0.002   HIS A 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00806 (12710)
  covalent geometry    : angle       0.96318 (17887)
  hydrogen bonds       : bond        0.05791 (  577)
  hydrogen bonds       : angle       4.90389 ( 1533)
  metal coordination   : bond        0.01359 (   16)
  metal coordination   : angle       2.90967 (   10)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 98
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7729 (tpp80) cc_final: 0.6890 (mmm-85)
REVERT: A   96 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7632 (ttp-170)
REVERT: A  206 LYS cc_start: 0.7113 (mtpp) cc_final: 0.6643 (ttpt)
REVERT: A  373 MET cc_start: 0.8812 (mtp) cc_final: 0.8306 (mtp)
REVERT: A  400 GLU cc_start: 0.8481 (tt0) cc_final: 0.8170 (tt0)
REVERT: A  596 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8063 (ttpp)
REVERT: A  607 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7841 (m-30)
REVERT: A  618 MET cc_start: 0.8867 (tpp) cc_final: 0.8616 (tpp)
REVERT: A  697 GLU cc_start: 0.8822 (mp0) cc_final: 0.8293 (mp0)
REVERT: A  834 ARG cc_start: 0.8677 (mtp85) cc_final: 0.7930 (mtm-85)
REVERT: A  954 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8895 (tt)
REVERT: A 1009 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7758 (ttpp)
REVERT: A 1015 VAL cc_start: 0.8689 (t) cc_final: 0.8343 (m)
REVERT: A 1059 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8023 (p90)
  outliers start: 44
  outliers final: 30
  residues processed: 130
  average time/residue: 0.1235
  time to fit residues: 22.8204
Evaluate side-chains
  121 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 86
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue   96 ARG
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  538 ASP
Chi-restraints excluded: chain A residue  547 MET
Chi-restraints excluded: chain A residue  589 ASN
Chi-restraints excluded: chain A residue  607 ASP
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  764 CYS
Chi-restraints excluded: chain A residue  784 SER
Chi-restraints excluded: chain A residue  835 ILE
Chi-restraints excluded: chain A residue  843 TYR
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain A residue  981 LYS
Chi-restraints excluded: chain A residue 1009 LYS
Chi-restraints excluded: chain A residue 1020 VAL
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1051 THR
Chi-restraints excluded: chain A residue 1059 PHE
Chi-restraints excluded: chain A residue 1078 THR
Chi-restraints excluded: chain A residue 1120 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 106 optimal weight:    0.0170
   chunk 12 optimal weight:   20.0000
   chunk 35 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 98 optimal weight:    9.9990
   chunk 112 optimal weight:    4.9990
   chunk 61 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 99 optimal weight:    5.9990
   chunk 104 optimal weight:    0.9980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 589 ASN
A 903 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.152124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.111924 restraints weight = 18998.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 1.78
r_work: 0.3231 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  12726  Z= 0.150
  Angle     :  0.870  40.104  17897  Z= 0.394
  Chirality :  0.059   1.982   2042
  Planarity :  0.004   0.038   1718
  Dihedral  : 25.574 178.557   3123
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  5.26 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 20.41 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.26), residues: 1103
  helix:  1.67 (0.23), residues: 542
  sheet: -0.72 (0.49), residues: 84
  loop : -1.26 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1038 
 TYR   0.011   0.002   TYR A 330 
 PHE   0.013   0.001   PHE A 908 
 TRP   0.008   0.001   TRP A 521 
 HIS   0.004   0.001   HIS A 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (12710)
  covalent geometry    : angle       0.86810 (17887)
  hydrogen bonds       : bond        0.04693 (  577)
  hydrogen bonds       : angle       4.66847 ( 1533)
  metal coordination   : bond        0.00883 (   16)
  metal coordination   : angle       2.28801 (   10)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7559 (tpp80) cc_final: 0.6908 (mmm-85)
REVERT: A  373 MET cc_start: 0.8803 (mtp) cc_final: 0.8238 (mtp)
REVERT: A  400 GLU cc_start: 0.8430 (tt0) cc_final: 0.8125 (tt0)
REVERT: A  596 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8002 (ttpp)
REVERT: A  697 GLU cc_start: 0.8724 (mp0) cc_final: 0.8460 (mp0)
REVERT: A  834 ARG cc_start: 0.8566 (mtp85) cc_final: 0.7875 (mtm-85)
REVERT: A  957 GLN cc_start: 0.8431 (mm110) cc_final: 0.8188 (mm110)
REVERT: A  981 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7908 (mmmm)
REVERT: A 1001 ARG cc_start: 0.6773 (mmt180) cc_final: 0.6304 (mmt90)
REVERT: A 1059 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7676 (p90)
  outliers start: 33
  outliers final: 21
  residues processed: 128
  average time/residue: 0.1267
  time to fit residues: 22.7527
Evaluate side-chains
  121 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain A residue  538 ASP
Chi-restraints excluded: chain A residue  589 ASN
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  764 CYS
Chi-restraints excluded: chain A residue  784 SER
Chi-restraints excluded: chain A residue  835 ILE
Chi-restraints excluded: chain A residue  843 TYR
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue  977 LYS
Chi-restraints excluded: chain A residue  981 LYS
Chi-restraints excluded: chain A residue 1059 PHE
Chi-restraints excluded: chain A residue 1120 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 80 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 119 optimal weight:   10.0000
   chunk 114 optimal weight:    7.9990
   chunk 105 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 116 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0030
   chunk 82 optimal weight:    8.9990
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 589 ASN
A 903 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.152957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.113405 restraints weight = 19084.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.86
r_work: 0.3227 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  12726  Z= 0.149
  Angle     :  0.866  40.145  17897  Z= 0.388
  Chirality :  0.058   1.979   2042
  Planarity :  0.004   0.041   1718
  Dihedral  : 25.506 179.480   3123
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  5.80 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 20.51 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.26), residues: 1103
  helix:  1.71 (0.22), residues: 547
  sheet: -0.77 (0.49), residues: 84
  loop : -1.21 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1038 
 TYR   0.010   0.001   TYR A 723 
 PHE   0.013   0.001   PHE A 908 
 TRP   0.008   0.001   TRP A 661 
 HIS   0.004   0.001   HIS A 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (12710)
  covalent geometry    : angle       0.86484 (17887)
  hydrogen bonds       : bond        0.04508 (  577)
  hydrogen bonds       : angle       4.49873 ( 1533)
  metal coordination   : bond        0.00799 (   16)
  metal coordination   : angle       2.07146 (   10)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7368 (tpp80) cc_final: 0.6781 (mmm-85)
REVERT: A  112 GLN cc_start: 0.8257 (mt0) cc_final: 0.7969 (mt0)
REVERT: A  373 MET cc_start: 0.8774 (mtp) cc_final: 0.8180 (mtp)
REVERT: A  400 GLU cc_start: 0.8256 (tt0) cc_final: 0.7975 (tt0)
REVERT: A  589 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8530 (t0)
REVERT: A  596 LYS cc_start: 0.8375 (mmmt) cc_final: 0.7962 (ttpp)
REVERT: A  697 GLU cc_start: 0.8579 (mp0) cc_final: 0.8299 (mp0)
REVERT: A  834 ARG cc_start: 0.8431 (mtp85) cc_final: 0.7797 (mtm-85)
REVERT: A  957 GLN cc_start: 0.8332 (mm110) cc_final: 0.8118 (mm110)
REVERT: A  981 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7821 (mmmm)
REVERT: A 1001 ARG cc_start: 0.6737 (mmt180) cc_final: 0.6261 (mmt90)
REVERT: A 1040 TYR cc_start: 0.7190 (m-80) cc_final: 0.6402 (m-80)
REVERT: A 1059 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7584 (p90)
  outliers start: 31
  outliers final: 24
  residues processed: 129
  average time/residue: 0.1304
  time to fit residues: 23.2540
Evaluate side-chains
  126 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  538 ASP
Chi-restraints excluded: chain A residue  589 ASN
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  764 CYS
Chi-restraints excluded: chain A residue  784 SER
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  835 ILE
Chi-restraints excluded: chain A residue  843 TYR
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue  977 LYS
Chi-restraints excluded: chain A residue  981 LYS
Chi-restraints excluded: chain A residue 1044 THR
Chi-restraints excluded: chain A residue 1059 PHE
Chi-restraints excluded: chain A residue 1120 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 12 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 95 optimal weight:    0.5980
   chunk 88 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   chunk 71 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 492 GLN
A 589 ASN
A 878 HIS
** A1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.148894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.108906 restraints weight = 19016.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.01
r_work: 0.3153 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  12726  Z= 0.278
  Angle     :  0.918  40.345  17897  Z= 0.418
  Chirality :  0.061   1.967   2042
  Planarity :  0.005   0.040   1718
  Dihedral  : 25.574 179.087   3123
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.80 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 19.90 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.25), residues: 1103
  helix:  1.49 (0.22), residues: 546
  sheet: -0.97 (0.47), residues: 84
  loop : -1.29 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  96 
 TYR   0.013   0.002   TYR A 723 
 PHE   0.018   0.002   PHE A 644 
 TRP   0.008   0.002   TRP A 856 
 HIS   0.007   0.001   HIS A 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00641 (12710)
  covalent geometry    : angle       0.91589 (17887)
  hydrogen bonds       : bond        0.05160 (  577)
  hydrogen bonds       : angle       4.67414 ( 1533)
  metal coordination   : bond        0.01048 (   16)
  metal coordination   : angle       2.52071 (   10)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 101
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7476 (tpp80) cc_final: 0.6804 (mmm-85)
REVERT: A  373 MET cc_start: 0.8784 (mtp) cc_final: 0.8193 (mtp)
REVERT: A  400 GLU cc_start: 0.8246 (tt0) cc_final: 0.7946 (tt0)
REVERT: A  596 LYS cc_start: 0.8434 (mmmt) cc_final: 0.8025 (ttpp)
REVERT: A  607 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7763 (m-30)
REVERT: A  697 GLU cc_start: 0.8607 (mp0) cc_final: 0.8053 (mp0)
REVERT: A  772 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8752 (m)
REVERT: A  834 ARG cc_start: 0.8497 (mtp85) cc_final: 0.7839 (mtm-85)
REVERT: A  957 GLN cc_start: 0.8281 (mm110) cc_final: 0.7989 (mm110)
REVERT: A  981 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7838 (mmmm)
REVERT: A 1001 ARG cc_start: 0.6821 (mmt180) cc_final: 0.6399 (mmt90)
REVERT: A 1040 TYR cc_start: 0.7482 (m-80) cc_final: 0.7264 (m-80)
REVERT: A 1046 GLN cc_start: 0.7504 (mp10) cc_final: 0.7196 (mt0)
REVERT: A 1059 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7886 (p90)
  outliers start: 38
  outliers final: 28
  residues processed: 127
  average time/residue: 0.1240
  time to fit residues: 22.1106
Evaluate side-chains
  129 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  376 ASN
Chi-restraints excluded: chain A residue  538 ASP
Chi-restraints excluded: chain A residue  607 ASP
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  764 CYS
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  784 SER
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  835 ILE
Chi-restraints excluded: chain A residue  843 TYR
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue  977 LYS
Chi-restraints excluded: chain A residue  981 LYS
Chi-restraints excluded: chain A residue 1044 THR
Chi-restraints excluded: chain A residue 1059 PHE
Chi-restraints excluded: chain A residue 1074 GLU
Chi-restraints excluded: chain A residue 1120 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 19 optimal weight:    8.9990
   chunk 101 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0980
   chunk 89 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 903 GLN
A1039 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.152604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.112108 restraints weight = 18986.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.91
r_work: 0.3234 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3096
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  12726  Z= 0.149
  Angle     :  0.863  40.146  17897  Z= 0.388
  Chirality :  0.058   1.978   2042
  Planarity :  0.004   0.042   1718
  Dihedral  : 25.507 179.101   3123
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.99 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.42 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.26), residues: 1103
  helix:  1.64 (0.22), residues: 551
  sheet: -0.76 (0.48), residues: 84
  loop : -1.16 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1038 
 TYR   0.011   0.001   TYR A 594 
 PHE   0.013   0.001   PHE A 908 
 TRP   0.009   0.001   TRP A 521 
 HIS   0.004   0.001   HIS A 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12710)
  covalent geometry    : angle       0.86138 (17887)
  hydrogen bonds       : bond        0.04409 (  577)
  hydrogen bonds       : angle       4.48293 ( 1533)
  metal coordination   : bond        0.00886 (   16)
  metal coordination   : angle       2.18057 (   10)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7436 (tpp80) cc_final: 0.6916 (mmm-85)
REVERT: A  239 ASN cc_start: 0.8111 (p0) cc_final: 0.7757 (t0)
REVERT: A  373 MET cc_start: 0.8805 (mtp) cc_final: 0.8257 (mtp)
REVERT: A  596 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8000 (ttpp)
REVERT: A  697 GLU cc_start: 0.8767 (mp0) cc_final: 0.8507 (mp0)
REVERT: A  834 ARG cc_start: 0.8566 (mtp85) cc_final: 0.7863 (mtm-85)
REVERT: A 1001 ARG cc_start: 0.6754 (mmt180) cc_final: 0.6378 (mmt90)
REVERT: A 1046 GLN cc_start: 0.7364 (mp10) cc_final: 0.7091 (mt0)
REVERT: A 1059 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7690 (p90)
  outliers start: 27
  outliers final: 23
  residues processed: 121
  average time/residue: 0.1308
  time to fit residues: 22.0740
Evaluate side-chains
  118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  538 ASP
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  764 CYS
Chi-restraints excluded: chain A residue  784 SER
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  835 ILE
Chi-restraints excluded: chain A residue  843 TYR
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue  977 LYS
Chi-restraints excluded: chain A residue 1059 PHE
Chi-restraints excluded: chain A residue 1120 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 116 optimal weight:    6.9990
   chunk 105 optimal weight:    0.6980
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 957 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.151095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.111636 restraints weight = 18978.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 1.81
r_work: 0.3201 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  12726  Z= 0.191
  Angle     :  0.888  40.191  17897  Z= 0.398
  Chirality :  0.059   1.972   2042
  Planarity :  0.005   0.041   1718
  Dihedral  : 25.447 178.928   3123
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.62 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 21.02 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.26), residues: 1103
  helix:  1.64 (0.22), residues: 548
  sheet: -0.76 (0.49), residues: 84
  loop : -1.13 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1038 
 TYR   0.011   0.002   TYR A 723 
 PHE   0.014   0.001   PHE A 908 
 TRP   0.008   0.001   TRP A 233 
 HIS   0.005   0.001   HIS A 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 (12710)
  covalent geometry    : angle       0.88698 (17887)
  hydrogen bonds       : bond        0.04601 (  577)
  hydrogen bonds       : angle       4.49179 ( 1533)
  metal coordination   : bond        0.00779 (   16)
  metal coordination   : angle       2.16585 (   10)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 96
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7293 (tpp80) cc_final: 0.6826 (mmm-85)
REVERT: A  239 ASN cc_start: 0.8004 (p0) cc_final: 0.7693 (t0)
REVERT: A  373 MET cc_start: 0.8768 (mtp) cc_final: 0.8216 (mtp)
REVERT: A  400 GLU cc_start: 0.8243 (tt0) cc_final: 0.7947 (tt0)
REVERT: A  596 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7961 (ttpp)
REVERT: A  697 GLU cc_start: 0.8560 (mp0) cc_final: 0.8276 (mp0)
REVERT: A  772 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8744 (m)
REVERT: A  834 ARG cc_start: 0.8455 (mtp85) cc_final: 0.7814 (mtm-85)
REVERT: A  981 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7854 (mmmm)
REVERT: A 1001 ARG cc_start: 0.6828 (mmt180) cc_final: 0.6406 (mmt90)
REVERT: A 1046 GLN cc_start: 0.7449 (mp10) cc_final: 0.7188 (mt0)
REVERT: A 1059 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7677 (p90)
  outliers start: 34
  outliers final: 28
  residues processed: 121
  average time/residue: 0.1272
  time to fit residues: 21.9029
Evaluate side-chains
  127 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 96
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  538 ASP
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  764 CYS
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  784 SER
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  835 ILE
Chi-restraints excluded: chain A residue  843 TYR
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue  977 LYS
Chi-restraints excluded: chain A residue  981 LYS
Chi-restraints excluded: chain A residue 1051 THR
Chi-restraints excluded: chain A residue 1059 PHE
Chi-restraints excluded: chain A residue 1120 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 95 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 99 optimal weight:    7.9990
   chunk 87 optimal weight:    0.8980
   chunk 12 optimal weight:    9.9990
   chunk 109 optimal weight:    0.8980
   chunk 118 optimal weight:    7.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 903 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.152398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.112685 restraints weight = 19189.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.84
r_work: 0.3218 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12726  Z= 0.163
  Angle     :  0.877  40.123  17897  Z= 0.391
  Chirality :  0.058   1.974   2042
  Planarity :  0.004   0.042   1718
  Dihedral  : 25.393 178.594   3123
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.35 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 21.12 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.26), residues: 1103
  helix:  1.68 (0.22), residues: 551
  sheet: -0.67 (0.49), residues: 84
  loop : -1.09 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1038 
 TYR   0.010   0.002   TYR A 723 
 PHE   0.013   0.001   PHE A 908 
 TRP   0.008   0.001   TRP A 661 
 HIS   0.004   0.001   HIS A 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (12710)
  covalent geometry    : angle       0.87571 (17887)
  hydrogen bonds       : bond        0.04390 (  577)
  hydrogen bonds       : angle       4.43500 ( 1533)
  metal coordination   : bond        0.00766 (   16)
  metal coordination   : angle       2.10701 (   10)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 100
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7241 (tpp80) cc_final: 0.6813 (mmm-85)
REVERT: A  239 ASN cc_start: 0.7923 (p0) cc_final: 0.7667 (t0)
REVERT: A  373 MET cc_start: 0.8775 (mtp) cc_final: 0.8232 (mtp)
REVERT: A  400 GLU cc_start: 0.8266 (tt0) cc_final: 0.7961 (tt0)
REVERT: A  596 LYS cc_start: 0.8391 (mmmt) cc_final: 0.7944 (ttpp)
REVERT: A  697 GLU cc_start: 0.8535 (mp0) cc_final: 0.8259 (mp0)
REVERT: A  772 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8741 (m)
REVERT: A  834 ARG cc_start: 0.8457 (mtp85) cc_final: 0.7813 (mtm-85)
REVERT: A  975 MET cc_start: 0.8921 (ttm) cc_final: 0.8686 (mtp)
REVERT: A 1001 ARG cc_start: 0.6859 (mmt180) cc_final: 0.6450 (mmt90)
REVERT: A 1046 GLN cc_start: 0.7395 (mp10) cc_final: 0.7153 (mt0)
REVERT: A 1059 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7652 (p90)
  outliers start: 31
  outliers final: 27
  residues processed: 120
  average time/residue: 0.1203
  time to fit residues: 20.4932
Evaluate side-chains
  124 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  304 CYS
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  538 ASP
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  647 SER
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  764 CYS
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  784 SER
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  835 ILE
Chi-restraints excluded: chain A residue  843 TYR
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue 1044 THR
Chi-restraints excluded: chain A residue 1051 THR
Chi-restraints excluded: chain A residue 1059 PHE
Chi-restraints excluded: chain A residue 1120 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 119 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 113 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 345 GLN
** A 354 ASN ** 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 = 0.3932 r_free = 0.3932 target = 0.150498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.110908 restraints weight = 18951.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.81
r_work: 0.3189 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  12726  Z= 0.216
  Angle     :  0.896  40.102  17897  Z= 0.403
  Chirality :  0.060   1.972   2042
  Planarity :  0.005   0.041   1718
  Dihedral  : 25.408 178.350   3123
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.80 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 21.32 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.25), residues: 1103
  helix:  1.61 (0.22), residues: 548
  sheet: -0.82 (0.48), residues: 84
  loop : -1.13 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1038 
 TYR   0.011   0.002   TYR A 723 
 PHE   0.015   0.002   PHE A 644 
 TRP   0.008   0.001   TRP A 901 
 HIS   0.005   0.001   HIS A 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 (12710)
  covalent geometry    : angle       0.89506 (17887)
  hydrogen bonds       : bond        0.04706 (  577)
  hydrogen bonds       : angle       4.50378 ( 1533)
  metal coordination   : bond        0.00818 (   16)
  metal coordination   : angle       2.25727 (   10)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3464.57 seconds
wall clock time: 59 minutes 58.62 seconds (3598.62 seconds total)