Starting phenix.real_space_refine
on Sat Sep 12 00:05:39 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7trd_26086/09_2026/7trd_26086.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7trd_26086/09_2026/7trd_26086.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7trd_26086/09_2026/7trd_26086.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7trd_26086/09_2026/7trd_26086.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7trd_26086/09_2026/7trd_26086.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7trd_26086/09_2026/7trd_26086.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7trd_26086/09_2026/7trd_26086.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7trd_26086/09_2026/7trd_26086.cif"
  }
  resolution = 3.3
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     224      5.49       5
     S      36      5.16       5
     C    6931      2.51       5
     N    2219      2.21       5
     O    2830      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12240
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 4605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 4605
          Classifications: {'RNAv2': 217}
          Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 21, 'rna3p_pur': 86, 'rna3p_pyr': 96}
          Link IDs: {'rna2p': 35, 'rna3p': 181}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 7488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 934, 7488
          Classifications: {'peptide': 934}
          Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 877}
          Chain breaks: 4
    Chain: "N"
      Number of atoms: 147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 147
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
  Time building chain proxies: 2.64, per 1000 atoms: 0.22
  Number of scatterers: 12240
  At special positions: 0
  Unit cell: (108.9, 122.1, 108.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     P     224     15.00
     O    2830      8.00
     N    2219      7.00
     C    6931      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: 0.82
  Conformation dependent library (CDL) restraints added in 432.3 milliseconds
  

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1766

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 8 sheets defined
      55.4% alpha, 15.2% beta
      64 base pairs and 96 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 18
      removed outlier: 3.604A  pdb=" N   ARG A  11 " --> pdb=" O   CYS A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 44 through 53
    Processing helix  chain 'A' and resid 76 through 92
    Processing helix  chain 'A' and resid 125 through 134
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 146 through 156
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.839A  pdb=" N   LEU A 178 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 332
      removed outlier: 3.999A  pdb=" N   LEU A 332 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 329 through 332'
    Processing helix  chain 'A' and resid 345 through 350
    Processing helix  chain 'A' and resid 353 through 366
      removed outlier: 3.574A  pdb=" N   ALA A 357 " --> pdb=" O   SER A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
    Processing helix  chain 'A' and resid 389 through 401
      removed outlier: 4.037A  pdb=" N   PHE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 413
      removed outlier: 3.782A  pdb=" N   LEU A 408 " --> pdb=" O   PRO A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 454
      removed outlier: 3.781A  pdb=" N   GLN A 454 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 471
      removed outlier: 3.716A  pdb=" N   ARG A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 3.506A  pdb=" N   GLU A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 517 through 521
      removed outlier: 3.655A  pdb=" N   LEU A 520 " --> pdb=" O   CYS A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 560
      removed outlier: 3.764A  pdb=" N   HIS A 534 " --> pdb=" O   PRO A 530 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   VAL A 553 " --> pdb=" O   MET A 549 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   VAL A 554 " --> pdb=" O   SER A 550 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   PHE A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 596
      removed outlier: 4.387A  pdb=" N   ILE A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLY A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL A 596 " --> pdb=" O   HIS A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 612
      removed outlier: 3.515A  pdb=" N   GLU A 611 " --> pdb=" O   ARG A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 672
      removed outlier: 3.531A  pdb=" N   SER A 656 " --> pdb=" O   GLU A 652 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ARG A 672 " --> pdb=" O   GLU A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 677
      removed outlier: 3.651A  pdb=" N   LEU A 676 " --> pdb=" O   PRO A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 698
      removed outlier: 3.762A  pdb=" N   ILE A 686 " --> pdb=" O   GLY A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 733
    Processing helix  chain 'A' and resid 765 through 769
      removed outlier: 4.006A  pdb=" N   LEU A 769 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 784
      removed outlier: 3.582A  pdb=" N   PHE A 776 " --> pdb=" O   TYR A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 815
    Processing helix  chain 'A' and resid 837 through 854
    Processing helix  chain 'A' and resid 876 through 890
    Processing helix  chain 'A' and resid 946 through 950
      removed outlier: 3.789A  pdb=" N   ALA A 950 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 958
      removed outlier: 4.052A  pdb=" N   LEU A 958 " --> pdb=" O   ARG A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 982
    Processing helix  chain 'A' and resid 983 through 988
    Processing helix  chain 'A' and resid 993 through 1017
    Processing helix  chain 'A' and resid 1024 through 1027
    Processing helix  chain 'A' and resid 1028 through 1051
      removed outlier: 4.120A  pdb=" N   PHE A1032 " --> pdb=" O   ASN A1028 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   TYR A1044 " --> pdb=" O   ALA A1040 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASN A1051 " --> pdb=" O   LEU A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1082
      removed outlier: 4.323A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN A1071 " --> pdb=" O   SER A1067 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   TRP A1072 " --> pdb=" O   GLU A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      removed outlier: 3.651A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
      Proline residue:  A1091  - end of helix
      removed outlier: 4.508A  pdb=" N   GLY A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   SER A1095 " --> pdb=" O   PRO A1091 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ARG A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LYS A1106 " --> pdb=" O   GLN A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1108 through 1119
      removed outlier: 3.712A  pdb=" N   ALA A1119 " --> pdb=" O   LEU A1115 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23
      removed outlier: 6.418A  pdb=" N   LEU A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 160 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 168 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 10.472A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 14.579A  pdb=" N   CYS A 171 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR A 744 " --> pdb=" O   LYS A 760 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23
      removed outlier: 6.418A  pdb=" N   LEU A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 160 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 168 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 10.472A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 14.579A  pdb=" N   CYS A 171 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA6, first strand: chain 'A' and resid 598 through 600
      removed outlier: 6.601A  pdb=" N   SER A 619 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 862 through 865
      removed outlier: 3.640A  pdb=" N   VAL A 904 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ASP A 712 " --> pdb=" O   LYS A 902 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   LYS A 902 " --> pdb=" O   ASP A 712 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 930

    396 hydrogen bonds defined for protein.
    1131 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      174 hydrogen bonds
      332 hydrogen bond angles
      0 basepair planarities
      64 basepair parallelities
      96 stacking parallelities
  Total time for adding SS restraints: 2.70

  Time building geometry restraints manager: 1.11 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: 2612
        1.33 -     1.45: 3958
        1.45 -     1.57: 5907
        1.57 -     1.69: 444
        1.69 -     1.81: 47
  Bond restraints: 12968
  Sorted by residual:
  bond pdb=" C   LYS A 973 "
       pdb=" N   LEU A 974 "
    ideal  model  delta    sigma   weight residual
    1.334  1.384 -0.049 1.27e-02 6.20e+03 1.50e+01
  bond pdb=" N   VAL A 697 "
       pdb=" CA  VAL A 697 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.037 1.21e-02 6.83e+03 9.11e+00
  bond pdb=" N   VAL A 127 "
       pdb=" CA  VAL A 127 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.97e+00
  bond pdb=" C3'  DT N  13 "
       pdb=" C2'  DT N  13 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 8.00e-03 1.56e+04 7.68e+00
  bond pdb=" N   ASN A 125 "
       pdb=" CA  ASN A 125 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.031 1.22e-02 6.72e+03 6.26e+00
  ... (remaining 12963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 17301
        1.52 -     3.05: 1079
        3.05 -     4.57: 206
        4.57 -     6.09: 57
        6.09 -     7.61: 1
  Bond angle restraints: 18644
  Sorted by residual:
  angle pdb=" O   LYS A 973 "
        pdb=" C   LYS A 973 "
        pdb=" N   LEU A 974 "
      ideal   model   delta    sigma   weight residual
     122.07  117.19    4.88 1.03e+00 9.43e-01 2.25e+01
  angle pdb=" N   VAL A 596 "
        pdb=" CA  VAL A 596 "
        pdb=" C   VAL A 596 "
      ideal   model   delta    sigma   weight residual
     112.43  108.61    3.82 9.20e-01 1.18e+00 1.73e+01
  angle pdb=" N3   DT N  13 "
        pdb=" C4   DT N  13 "
        pdb=" O4   DT N  13 "
      ideal   model   delta    sigma   weight residual
     119.90  122.38   -2.48 6.00e-01 2.78e+00 1.70e+01
  angle pdb=" N3   DT N  12 "
        pdb=" C4   DT N  12 "
        pdb=" O4   DT N  12 "
      ideal   model   delta    sigma   weight residual
     119.90  122.37   -2.47 6.00e-01 2.78e+00 1.69e+01
  angle pdb=" N3   DT N  14 "
        pdb=" C4   DT N  14 "
        pdb=" O4   DT N  14 "
      ideal   model   delta    sigma   weight residual
     119.90  122.33   -2.43 6.00e-01 2.78e+00 1.64e+01
  ... (remaining 18639 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.35: 6306
       22.35 -    44.70: 652
       44.70 -    67.05: 290
       67.05 -    89.40: 54
       89.40 -   111.75: 1
  Dihedral angle restraints: 7303
    sinusoidal: 4580
      harmonic: 2723
  Sorted by residual:
  dihedral pdb=" C4'   A B 281 "
           pdb=" C3'   A B 281 "
           pdb=" C2'   A B 281 "
           pdb=" C1'   A B 281 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -38.94   75.29     1      3.10e+00 1.04e-01 7.45e+02
  dihedral pdb=" C4'   A B 301 "
           pdb=" C3'   A B 301 "
           pdb=" C2'   A B 301 "
           pdb=" C1'   A B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -38.29   74.63     1      3.10e+00 1.04e-01 7.34e+02
  dihedral pdb=" C4'   G B 251 "
           pdb=" C3'   G B 251 "
           pdb=" C2'   G B 251 "
           pdb=" C1'   G B 251 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -37.34   73.69     1      3.10e+00 1.04e-01 7.18e+02
  ... (remaining 7300 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 1913
       0.095 -    0.190: 81
       0.190 -    0.285: 284
       0.285 -    0.380: 6
       0.380 -    0.475: 1
  Chirality restraints: 2285
  Sorted by residual:
  chirality pdb=" P     G B 130 "
            pdb=" OP1   G B 130 "
            pdb=" OP2   G B 130 "
            pdb=" O5'   G B 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.65   -0.47 2.00e-01 2.50e+01 5.64e+00
  chirality pdb=" C2'   A B 281 "
            pdb=" C3'   A B 281 "
            pdb=" O2'   A B 281 "
            pdb=" C1'   A B 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.48   -0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" C2'   C B 256 "
            pdb=" C3'   C B 256 "
            pdb=" O2'   C B 256 "
            pdb=" C1'   C B 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.48   -0.31 2.00e-01 2.50e+01 2.36e+00
  ... (remaining 2282 not shown)

  Planarity restraints: 1542
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 130 "   -0.001 2.00e-02 2.50e+03   4.15e-02 5.17e+01
        pdb=" N9    G B 130 "    0.002 2.00e-02 2.50e+03
        pdb=" C8    G B 130 "   -0.010 2.00e-02 2.50e+03
        pdb=" N7    G B 130 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G B 130 "    0.036 2.00e-02 2.50e+03
        pdb=" C6    G B 130 "   -0.105 2.00e-02 2.50e+03
        pdb=" O6    G B 130 "    0.069 2.00e-02 2.50e+03
        pdb=" N1    G B 130 "   -0.039 2.00e-02 2.50e+03
        pdb=" C2    G B 130 "    0.046 2.00e-02 2.50e+03
        pdb=" N2    G B 130 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    G B 130 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    G B 130 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B 129 "    0.003 2.00e-02 2.50e+03   3.20e-02 2.82e+01
        pdb=" N9    A B 129 "   -0.003 2.00e-02 2.50e+03
        pdb=" C8    A B 129 "   -0.008 2.00e-02 2.50e+03
        pdb=" N7    A B 129 "   -0.015 2.00e-02 2.50e+03
        pdb=" C5    A B 129 "    0.075 2.00e-02 2.50e+03
        pdb=" C6    A B 129 "    0.020 2.00e-02 2.50e+03
        pdb=" N6    A B 129 "   -0.014 2.00e-02 2.50e+03
        pdb=" N1    A B 129 "   -0.045 2.00e-02 2.50e+03
        pdb=" C2    A B 129 "    0.031 2.00e-02 2.50e+03
        pdb=" N3    A B 129 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A B 129 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B 131 "   -0.015 2.00e-02 2.50e+03   3.41e-02 2.62e+01
        pdb=" N1    C B 131 "   -0.012 2.00e-02 2.50e+03
        pdb=" C2    C B 131 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    C B 131 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3    C B 131 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    C B 131 "    0.077 2.00e-02 2.50e+03
        pdb=" N4    C B 131 "   -0.064 2.00e-02 2.50e+03
        pdb=" C5    C B 131 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    C B 131 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1539 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 1470
        2.74 -     3.28: 11066
        3.28 -     3.82: 21444
        3.82 -     4.36: 24209
        4.36 -     4.90: 37863
  Nonbonded interactions: 96052
  Sorted by model distance:
  nonbonded pdb=" O   LEU A1079 "
            pdb=" OG1 THR A1083 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O2'   G B  71 "
            pdb=" OP1   C B  72 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER A 619 "
            pdb=" O   ASN A 635 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O2'   A B 175 "
            pdb=" OP1   A B 176 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O2'   U B 314 "
            pdb=" OE2 GLU A 538 "
     model   vdw
     2.293 3.040
  ... (remaining 96047 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.160
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
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   0.049  12968  Z= 0.232
  Angle     :  0.857   7.614  18644  Z= 0.428
  Chirality :  0.093   0.475   2285
  Planarity :  0.005   0.042   1542
  Dihedral  : 19.706 111.754   5537
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.86 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.28), residues: 924
  helix:  1.00 (0.26), residues: 443
  sheet: -0.29 (0.51), residues: 93
  loop : -1.25 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 470 
 TYR   0.009   0.001   TYR A 168 
 PHE   0.026   0.002   PHE A1021 
 TRP   0.016   0.001   TRP A 581 
 HIS   0.011   0.001   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00410 /  0.23 (12968)
  covalent geometry    : angle       0.85688 /  0.43 (18644)
  hydrogen bonds       : bond        0.13344 /  7.27 (  556)
  hydrogen bonds       : angle       5.61174 /  2.35 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4197 (mmp) cc_final: 0.3919 (mmm)
REVERT: A  700 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7503 (mt0)
REVERT: A 1059 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8219 (ttmm)
  outliers start: 1
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1499
  time to fit residues: 9.8548
Evaluate side-chains
  32 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  700 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 779 HIS
** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1023 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.145231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.088820 restraints weight = 23067.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 2.21
r_work: 0.3016 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12968  Z= 0.210
  Angle     :  1.351  21.735  18644  Z= 0.531
  Chirality :  0.118   1.174   2285
  Planarity :  0.005   0.046   1542
  Dihedral  : 18.743 143.139   3721
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  5.54 %
    Favored  : 94.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.29), residues: 924
  helix:  1.29 (0.25), residues: 451
  sheet: -0.21 (0.48), residues: 103
  loop : -1.10 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  15 
 TYR   0.008   0.001   TYR A 122 
 PHE   0.015   0.001   PHE A1021 
 TRP   0.011   0.001   TRP A 581 
 HIS   0.009   0.001   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.21 (12968)
  covalent geometry    : angle       1.35065 /  0.53 (18644)
  hydrogen bonds       : bond        0.05289 /  2.79 (  556)
  hydrogen bonds       : angle       4.33527 /  1.79 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4801 (mmp) cc_final: 0.4507 (mmm)
REVERT: A 1059 LYS cc_start: 0.8634 (ttmt) cc_final: 0.8308 (ttmt)
  outliers start: 3
  outliers final: 1
  residues processed: 41
  average time/residue: 0.0931
  time to fit residues: 5.9852
Evaluate side-chains
  35 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  779 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0040
   chunk 87 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 90 optimal weight:    0.0980
   overall best weight:    1.0198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 635 ASN
A 779 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.145759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.089271 restraints weight = 23186.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 2.22
r_work: 0.3026 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12968  Z= 0.157
  Angle     :  0.977  16.100  18644  Z= 0.393
  Chirality :  0.078   0.883   2285
  Planarity :  0.004   0.040   1542
  Dihedral  : 18.630 153.949   3718
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  7.27 %
    Favored  : 92.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.29), residues: 924
  helix:  1.50 (0.25), residues: 453
  sheet: -0.12 (0.48), residues: 103
  loop : -0.96 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  15 
 TYR   0.020   0.001   TYR A 168 
 PHE   0.014   0.001   PHE A 331 
 TRP   0.011   0.001   TRP A 581 
 HIS   0.035   0.002   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.16 (12968)
  covalent geometry    : angle       0.97731 /  0.39 (18644)
  hydrogen bonds       : bond        0.04810 /  2.52 (  556)
  hydrogen bonds       : angle       4.06821 /  1.67 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4902 (mmp) cc_final: 0.4651 (mmm)
REVERT: A 1059 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8350 (ttmm)
  outliers start: 4
  outliers final: 4
  residues processed: 42
  average time/residue: 0.0915
  time to fit residues: 6.1212
Evaluate side-chains
  40 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 37 optimal weight:    0.0870
   chunk 4 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 104 optimal weight:    0.7980
   chunk 63 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.6960

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  53 GLN
A 779 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.147107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.091331 restraints weight = 23342.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.19
r_work: 0.3083 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12968  Z= 0.134
  Angle     :  0.898  14.772  18644  Z= 0.362
  Chirality :  0.068   0.579   2285
  Planarity :  0.004   0.034   1542
  Dihedral  : 18.226 150.039   3718
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  8.74 %
    Favored  : 90.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.29), residues: 924
  helix:  1.69 (0.25), residues: 454
  sheet:  0.03 (0.49), residues: 96
  loop : -0.89 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 132 
 TYR   0.005   0.001   TYR A 122 
 PHE   0.012   0.001   PHE A 776 
 TRP   0.010   0.001   TRP A 581 
 HIS   0.031   0.001   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.13 (12968)
  covalent geometry    : angle       0.89775 /  0.36 (18644)
  hydrogen bonds       : bond        0.04377 /  2.29 (  556)
  hydrogen bonds       : angle       3.91231 /  1.61 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4986 (mmp) cc_final: 0.4719 (mmm)
REVERT: A  536 LEU cc_start: 0.9106 (tp) cc_final: 0.8775 (tp)
REVERT: A 1059 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8377 (ttmt)
  outliers start: 6
  outliers final: 4
  residues processed: 43
  average time/residue: 0.0868
  time to fit residues: 5.9197
Evaluate side-chains
  41 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 32 optimal weight:    9.9990
   chunk 94 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 3 optimal weight:   20.0000
   chunk 75 optimal weight:    0.5980
   chunk 76 optimal weight:   20.0000
   chunk 88 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.4384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.145710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.089494 restraints weight = 23276.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 2.17
r_work: 0.3049 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12968  Z= 0.163
  Angle     :  0.882  14.693  18644  Z= 0.359
  Chirality :  0.066   0.570   2285
  Planarity :  0.004   0.034   1542
  Dihedral  : 18.112 149.592   3718
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  9.73 %
    Favored  : 89.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.29), residues: 924
  helix:  1.69 (0.25), residues: 455
  sheet:  0.12 (0.50), residues: 96
  loop : -0.88 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 132 
 TYR   0.006   0.001   TYR A 462 
 PHE   0.019   0.001   PHE A 331 
 TRP   0.009   0.001   TRP A 581 
 HIS   0.013   0.001   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.16 (12968)
  covalent geometry    : angle       0.88209 /  0.36 (18644)
  hydrogen bonds       : bond        0.04609 /  2.40 (  556)
  hydrogen bonds       : angle       3.90637 /  1.60 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4866 (mmp) cc_final: 0.4584 (mmm)
REVERT: A 1059 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8427 (ttmt)
  outliers start: 7
  outliers final: 5
  residues processed: 42
  average time/residue: 0.0954
  time to fit residues: 6.2585
Evaluate side-chains
  41 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  808 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 21 optimal weight:    9.9990
   chunk 105 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 32 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  86 GLN
A 779 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.146977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.090934 restraints weight = 23236.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 2.20
r_work: 0.3071 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12968  Z= 0.128
  Angle     :  0.850  14.309  18644  Z= 0.343
  Chirality :  0.064   0.545   2285
  Planarity :  0.004   0.033   1542
  Dihedral  : 17.993 148.735   3718
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 11.08 %
    Favored  : 88.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.29), residues: 924
  helix:  1.84 (0.25), residues: 455
  sheet:  0.22 (0.51), residues: 96
  loop : -0.87 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 132 
 TYR   0.006   0.001   TYR A 462 
 PHE   0.013   0.001   PHE A 331 
 TRP   0.010   0.001   TRP A 581 
 HIS   0.005   0.001   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.13 (12968)
  covalent geometry    : angle       0.85002 /  0.34 (18644)
  hydrogen bonds       : bond        0.04290 /  2.24 (  556)
  hydrogen bonds       : angle       3.78880 /  1.55 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4806 (mmp) cc_final: 0.4527 (mmm)
REVERT: A  536 LEU cc_start: 0.9122 (tp) cc_final: 0.8797 (tp)
REVERT: A 1059 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8418 (ttmt)
  outliers start: 5
  outliers final: 4
  residues processed: 43
  average time/residue: 0.0979
  time to fit residues: 6.5306
Evaluate side-chains
  43 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 15 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 3 optimal weight:   20.0000
   chunk 108 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   chunk 46 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.147198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.090966 restraints weight = 23273.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.19
r_work: 0.3075 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12968  Z= 0.128
  Angle     :  0.838  14.091  18644  Z= 0.340
  Chirality :  0.063   0.528   2285
  Planarity :  0.004   0.056   1542
  Dihedral  : 17.919 148.452   3718
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 11.95 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.29), residues: 924
  helix:  1.89 (0.25), residues: 454
  sheet:  0.22 (0.51), residues: 96
  loop : -0.87 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 132 
 TYR   0.006   0.001   TYR A 462 
 PHE   0.013   0.001   PHE A 331 
 TRP   0.010   0.001   TRP A 581 
 HIS   0.004   0.001   HIS A 609 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.13 (12968)
  covalent geometry    : angle       0.83812 /  0.34 (18644)
  hydrogen bonds       : bond        0.04258 /  2.22 (  556)
  hydrogen bonds       : angle       3.75729 /  1.54 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4846 (mmp) cc_final: 0.4571 (mmm)
REVERT: A  536 LEU cc_start: 0.9124 (tp) cc_final: 0.8791 (tp)
REVERT: A 1059 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8437 (ttmt)
  outliers start: 5
  outliers final: 5
  residues processed: 45
  average time/residue: 0.0881
  time to fit residues: 6.2675
Evaluate side-chains
  44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 22 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 112 optimal weight:    3.9990
   chunk 102 optimal weight:    0.8980
   chunk 9 optimal weight:   20.0000
   chunk 89 optimal weight:    0.8980
   chunk 33 optimal weight:    7.9990
   chunk 70 optimal weight:    3.9990
   chunk 110 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 687 HIS
A 779 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.147429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.091367 restraints weight = 23133.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.19
r_work: 0.3082 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12968  Z= 0.124
  Angle     :  0.823  13.837  18644  Z= 0.334
  Chirality :  0.062   0.509   2285
  Planarity :  0.004   0.033   1542
  Dihedral  : 17.847 147.820   3718
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 11.95 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.29), residues: 924
  helix:  1.95 (0.25), residues: 455
  sheet:  0.22 (0.50), residues: 96
  loop : -0.84 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 132 
 TYR   0.006   0.001   TYR A 462 
 PHE   0.013   0.001   PHE A 331 
 TRP   0.010   0.001   TRP A 581 
 HIS   0.014   0.001   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 (12968)
  covalent geometry    : angle       0.82336 /  0.33 (18644)
  hydrogen bonds       : bond        0.04162 /  2.17 (  556)
  hydrogen bonds       : angle       3.72833 /  1.53 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4951 (mmp) cc_final: 0.4671 (mmm)
REVERT: A  536 LEU cc_start: 0.9099 (tp) cc_final: 0.8764 (tp)
REVERT: A 1059 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8439 (ttmt)
  outliers start: 5
  outliers final: 4
  residues processed: 44
  average time/residue: 0.0846
  time to fit residues: 5.8614
Evaluate side-chains
  43 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 113 optimal weight:    0.0970
   chunk 65 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 11 optimal weight:   30.0000
   chunk 25 optimal weight:    0.7980
   chunk 107 optimal weight:    4.9990
   chunk 76 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0770
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.1940

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.146897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.090643 restraints weight = 23141.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.17
r_work: 0.3070 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
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      :  0.003   0.041  12968  Z= 0.138
  Angle     :  0.823  13.564  18644  Z= 0.335
  Chirality :  0.061   0.494   2285
  Planarity :  0.004   0.033   1542
  Dihedral  : 17.806 146.570   3718
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 12.56 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.29), residues: 924
  helix:  1.95 (0.25), residues: 455
  sheet:  0.25 (0.51), residues: 96
  loop : -0.85 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 132 
 TYR   0.007   0.001   TYR A 462 
 PHE   0.016   0.001   PHE A 331 
 TRP   0.010   0.001   TRP A 581 
 HIS   0.015   0.001   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.14 (12968)
  covalent geometry    : angle       0.82322 /  0.33 (18644)
  hydrogen bonds       : bond        0.04288 /  2.23 (  556)
  hydrogen bonds       : angle       3.70673 /  1.52 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4888 (mmp) cc_final: 0.4601 (mmm)
REVERT: A 1059 LYS cc_start: 0.8792 (ttmt) cc_final: 0.8460 (ttmt)
  outliers start: 6
  outliers final: 6
  residues processed: 42
  average time/residue: 0.1017
  time to fit residues: 6.8328
Evaluate side-chains
  44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 36 optimal weight:    0.5980
   chunk 10 optimal weight:   20.0000
   chunk 112 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 2 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.6184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.146329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.089965 restraints weight = 23187.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 2.17
r_work: 0.3054 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12968  Z= 0.163
  Angle     :  0.833  13.460  18644  Z= 0.339
  Chirality :  0.062   0.491   2285
  Planarity :  0.004   0.033   1542
  Dihedral  : 17.797 145.990   3718
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 12.68 %
    Favored  : 86.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.29), residues: 924
  helix:  1.92 (0.25), residues: 455
  sheet:  0.26 (0.51), residues: 96
  loop : -0.89 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 132 
 TYR   0.007   0.001   TYR A 462 
 PHE   0.018   0.001   PHE A 331 
 TRP   0.009   0.001   TRP A 581 
 HIS   0.017   0.001   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.16 (12968)
  covalent geometry    : angle       0.83283 /  0.34 (18644)
  hydrogen bonds       : bond        0.04416 /  2.30 (  556)
  hydrogen bonds       : angle       3.73547 /  1.53 ( 1463)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A  372 MET cc_start: 0.4914 (mmp) cc_final: 0.4628 (mmm)
REVERT: A 1059 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8460 (ttmt)
  outliers start: 6
  outliers final: 6
  residues processed: 40
  average time/residue: 0.1083
  time to fit residues: 6.8134
Evaluate side-chains
  42 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ASP
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   chunk 101 optimal weight:    0.7980
   chunk 6 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 83 optimal weight:    0.0980
   chunk 30 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.147489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.091389 restraints weight = 22998.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.17
r_work: 0.3084 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  12968  Z= 0.116
  Angle     :  0.810  13.375  18644  Z= 0.329
  Chirality :  0.060   0.478   2285
  Planarity :  0.004   0.033   1542
  Dihedral  : 17.763 146.069   3718
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 13.05 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.29), residues: 924
  helix:  2.01 (0.25), residues: 455
  sheet:  0.29 (0.51), residues: 96
  loop : -0.85 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 132 
 TYR   0.007   0.001   TYR A 462 
 PHE   0.012   0.001   PHE A 331 
 TRP   0.011   0.001   TRP A 581 
 HIS   0.025   0.001   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.12 (12968)
  covalent geometry    : angle       0.80973 /  0.33 (18644)
  hydrogen bonds       : bond        0.04142 /  2.16 (  556)
  hydrogen bonds       : angle       3.68716 /  1.51 ( 1463)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2726.63 seconds
wall clock time: 47 minutes 29.04 seconds (2849.04 seconds total)