Starting phenix.real_space_refine
on Wed Mar  4 23:50:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7z4e_14494/03_2026/7z4e_14494.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z4e_14494/03_2026/7z4e_14494.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7z4e_14494/03_2026/7z4e_14494.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z4e_14494/03_2026/7z4e_14494.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z4e_14494/03_2026/7z4e_14494.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z4e_14494/03_2026/7z4e_14494.cif"
  }
  resolution = 4.14
  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=   0.003 sd=   0.018
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 3728 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     138      5.49       5
     S      23      5.16       5
     C    8436      2.51       5
     N    2467      2.21       5
     O    3005      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14069
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 11089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1357, 11089
          Classifications: {'peptide': 1357}
          Link IDs: {'PTRANS': 35, 'TRANS': 1321}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 1884
          Classifications: {'RNA': 88}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 46, 'rna3p_pyr': 28}
          Link IDs: {'rna2p': 14, 'rna3p': 73}
    Chain: "C"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 587
          Classifications: {'DNA': 29}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 28}
    Chain: "D"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 509
          Inner-chain residues flagged as termini: ['pdbres=" DT D  -3 "']
          Classifications: {'DNA': 25}
          Modifications used: {'5*END': 2}
          Link IDs: {'rna3p': 24}
  Time building chain proxies: 3.10, per 1000 atoms: 0.22
  Number of scatterers: 14069
  At special positions: 0
  Unit cell: (94.9, 131.95, 122.2, 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      23     16.00
     P     138     15.00
     O    3005      8.00
     N    2467      7.00
     C    8436      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: 1.14
  Conformation dependent library (CDL) restraints added in 461.8 milliseconds
  

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2580

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 10 sheets defined
      53.6% alpha, 8.0% beta
      50 base pairs and 85 stacking pairs defined.
    Time for finding SS restraints: 1.71
  Creating SS restraints...
    Processing helix  chain 'B' and resid 59 through 94
      removed outlier: 4.121A  pdb=" N   ARG B  69 " --> pdb=" O   LYS B  65 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   LYS B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   ASN B  88 " --> pdb=" O   GLU B  84 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   GLU B  89 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 103
    Processing helix  chain 'B' and resid 121 through 132
    Processing helix  chain 'B' and resid 134 through 145
      removed outlier: 3.737A  pdb=" N   LEU B 138 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 164
      removed outlier: 3.737A  pdb=" N   PHE B 164 " --> pdb=" O   HIS B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 196
    Processing helix  chain 'B' and resid 207 through 214
    Processing helix  chain 'B' and resid 217 through 228
    Processing helix  chain 'B' and resid 236 through 247
    Processing helix  chain 'B' and resid 252 through 257
    Processing helix  chain 'B' and resid 270 through 283
    Processing helix  chain 'B' and resid 286 through 303
    Processing helix  chain 'B' and resid 317 through 343
    Processing helix  chain 'B' and resid 346 through 353
      removed outlier: 3.727A  pdb=" N   ASP B 353 " --> pdb=" O   GLU B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 364
    Processing helix  chain 'B' and resid 368 through 383
      Proline residue:  B 378  - end of helix
    Processing helix  chain 'B' and resid 386 through 395
    Processing helix  chain 'B' and resid 406 through 410
      removed outlier: 4.097A  pdb=" N   SER B 409 " --> pdb=" O   ASP B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 427
      removed outlier: 4.269A  pdb=" N   HIS B 415 " --> pdb=" O   PRO B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 436
    Processing helix  chain 'B' and resid 436 through 446
    Processing helix  chain 'B' and resid 477 through 482
      removed outlier: 3.525A  pdb=" N   VAL B 482 " --> pdb=" O   PHE B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 495
    Processing helix  chain 'B' and resid 512 through 525
    Processing helix  chain 'B' and resid 541 through 552
    Processing helix  chain 'B' and resid 560 through 568
      removed outlier: 3.686A  pdb=" N   TYR B 568 " --> pdb=" O   LEU B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 602
    Processing helix  chain 'B' and resid 603 through 609
    Processing helix  chain 'B' and resid 612 through 626
      removed outlier: 3.604A  pdb=" N   PHE B 626 " --> pdb=" O   THR B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 628 through 637
    Processing helix  chain 'B' and resid 638 through 640
      No H-bonds generated for 'chain 'B' and resid 638 through 640'
    Processing helix  chain 'B' and resid 644 through 654
    Processing helix  chain 'B' and resid 664 through 669
    Processing helix  chain 'B' and resid 678 through 685
    Processing helix  chain 'B' and resid 692 through 698
    Processing helix  chain 'B' and resid 702 through 713
      removed outlier: 4.450A  pdb=" N   GLU B 706 " --> pdb=" O   LEU B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 719 through 727
      removed outlier: 3.769A  pdb=" N   HIS B 723 " --> pdb=" O   SER B 719 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU B 727 " --> pdb=" O   HIS B 723 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 730 through 751
    Processing helix  chain 'B' and resid 776 through 792
    Processing helix  chain 'B' and resid 794 through 799
    Processing helix  chain 'B' and resid 803 through 807
    Processing helix  chain 'B' and resid 808 through 817
    Processing helix  chain 'B' and resid 832 through 836
    Processing helix  chain 'B' and resid 860 through 865
      removed outlier: 3.577A  pdb=" N   GLY B 865 " --> pdb=" O   LYS B 862 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 872 through 889
      removed outlier: 5.950A  pdb=" N   ASN B 881 " --> pdb=" O   LYS B 877 " (cutoff:3.500A)
      removed outlier: 5.766A  pdb=" N   TYR B 882 " --> pdb=" O   LYS B 878 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 893 through 901
    Processing helix  chain 'B' and resid 909 through 922
    Processing helix  chain 'B' and resid 926 through 940
    Processing helix  chain 'B' and resid 959 through 970
      removed outlier: 3.950A  pdb=" N   VAL B 963 " --> pdb=" O   LYS B 959 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 980 through 1001
      removed outlier: 4.345A  pdb=" N   ALA B 984 " --> pdb=" O   ASN B 980 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1004 through 1009
    Processing helix  chain 'B' and resid 1078 through 1088
    Processing helix  chain 'B' and resid 1127 through 1132
    Processing helix  chain 'B' and resid 1152 through 1155
    Processing helix  chain 'B' and resid 1170 through 1177
    Processing helix  chain 'B' and resid 1177 through 1186
    Processing helix  chain 'B' and resid 1191 through 1195
    Processing helix  chain 'B' and resid 1207 through 1209
      No H-bonds generated for 'chain 'B' and resid 1207 through 1209'
    Processing helix  chain 'B' and resid 1229 through 1240
    Processing helix  chain 'B' and resid 1248 through 1262
    Processing helix  chain 'B' and resid 1264 through 1281
    Processing helix  chain 'B' and resid 1283 through 1297
    Processing helix  chain 'B' and resid 1301 through 1313
    Processing helix  chain 'B' and resid 1314 through 1316
      No H-bonds generated for 'chain 'B' and resid 1314 through 1316'
    Processing helix  chain 'B' and resid 1340 through 1344
    Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 957
    Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46
      removed outlier: 3.519A  pdb=" N   ILE B  43 " --> pdb=" O   PHE B  32 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS B  45 " --> pdb=" O   LYS B  30 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS B  30 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
      removed outlier: 9.789A  pdb=" N   GLU B1357 " --> pdb=" O   LYS B  31 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   LYS B  33 " --> pdb=" O   GLU B1357 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   ARG B1359 " --> pdb=" O   LYS B  33 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   LEU B  35 " --> pdb=" O   ARG B1359 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   ASP B1361 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LEU B1203 " --> pdb=" O   ILE B1348 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   SER B1202 " --> pdb=" O   LEU B1214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509
      removed outlier: 5.541A  pdb=" N   LEU B 508 " --> pdb=" O   GLY B 660 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539
      removed outlier: 3.604A  pdb=" N   TYR B 529 " --> pdb=" O   ALA B 538 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 837 through 840
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1049 through 1050
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1063 through 1065
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1107 through 1111
      removed outlier: 6.668A  pdb=" N   SER B1109 " --> pdb=" O   ASP B1135 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   ASP B1135 " --> pdb=" O   SER B1109 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 1157 through 1167
      removed outlier: 3.516A  pdb=" N   GLU B1162 " --> pdb=" O   VAL B1145 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE B1166 " --> pdb=" O   TYR B1141 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   TYR B1141 " --> pdb=" O   ILE B1166 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE B1196 " --> pdb=" O   LEU B1144 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326

    517 hydrogen bonds defined for protein.
    1485 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      123 hydrogen bonds
      242 hydrogen bond angles
      0 basepair planarities
      50 basepair parallelities
      85 stacking parallelities
  Total time for adding SS restraints: 3.59

  Time building geometry restraints manager: 1.46 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.35: 4323
        1.35 -     1.50: 4657
        1.50 -     1.65: 5599
        1.65 -     1.80: 29
        1.80 -     1.95: 15
  Bond restraints: 14623
  Sorted by residual:
  bond pdb=" SD  MET B1021 "
       pdb=" CE  MET B1021 "
    ideal  model  delta    sigma   weight residual
    1.791  1.951 -0.160 2.50e-02 1.60e+03 4.10e+01
  bond pdb=" CG  MET B1021 "
       pdb=" SD  MET B1021 "
    ideal  model  delta    sigma   weight residual
    1.803  1.950 -0.147 2.50e-02 1.60e+03 3.46e+01
  bond pdb=" O3'   G A  43 "
       pdb=" P     U A  44 "
    ideal  model  delta    sigma   weight residual
    1.607  1.651 -0.044 1.50e-02 4.44e+03 8.51e+00
  bond pdb=" N   LYS B 163 "
       pdb=" CA  LYS B 163 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.54e+00
  bond pdb=" N   GLU B 102 "
       pdb=" CA  GLU B 102 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.33e-02 5.65e+03 6.69e+00
  ... (remaining 14618 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 19729
        1.44 -     2.89: 544
        2.89 -     4.33: 61
        4.33 -     5.78: 5
        5.78 -     7.22: 2
  Bond angle restraints: 20341
  Sorted by residual:
  angle pdb=" N   GLU B 627 "
        pdb=" CA  GLU B 627 "
        pdb=" C   GLU B 627 "
      ideal   model   delta    sigma   weight residual
     114.75  107.53    7.22 1.26e+00 6.30e-01 3.28e+01
  angle pdb=" C   ARG B 403 "
        pdb=" CA  ARG B 403 "
        pdb=" CB  ARG B 403 "
      ideal   model   delta    sigma   weight residual
     109.53  116.08   -6.55 1.65e+00 3.67e-01 1.58e+01
  angle pdb=" N   GLN B 402 "
        pdb=" CA  GLN B 402 "
        pdb=" C   GLN B 402 "
      ideal   model   delta    sigma   weight residual
     111.14  107.16    3.98 1.08e+00 8.57e-01 1.36e+01
  angle pdb=" N   ARG B 100 "
        pdb=" CA  ARG B 100 "
        pdb=" C   ARG B 100 "
      ideal   model   delta    sigma   weight residual
     110.97  107.40    3.57 1.09e+00 8.42e-01 1.08e+01
  angle pdb=" CA  LEU B1206 "
        pdb=" C   LEU B1206 "
        pdb=" N   GLU B1207 "
      ideal   model   delta    sigma   weight residual
     115.75  120.02   -4.27 1.34e+00 5.57e-01 1.02e+01
  ... (remaining 20336 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.26: 7925
       21.26 -    42.52: 548
       42.52 -    63.78: 350
       63.78 -    85.04: 45
       85.04 -   106.30: 6
  Dihedral angle restraints: 8874
    sinusoidal: 4884
      harmonic: 3990
  Sorted by residual:
  dihedral pdb=" O4'   U A  59 "
           pdb=" C1'   U A  59 "
           pdb=" N1    U A  59 "
           pdb=" C2    U A  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -66.06  -61.94     1      1.70e+01 3.46e-03 1.76e+01
  dihedral pdb=" O4'   G A  33 "
           pdb=" C1'   G A  33 "
           pdb=" N9    G A  33 "
           pdb=" C4    G A  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
      70.00   -2.44   72.44     1      2.00e+01 2.50e-03 1.68e+01
  dihedral pdb=" O4'   G A  82 "
           pdb=" C1'   G A  82 "
           pdb=" N9    G A  82 "
           pdb=" C4    G A  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -33.97  -56.03     1      2.00e+01 2.50e-03 1.06e+01
  ... (remaining 8871 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1783
       0.039 -    0.077: 411
       0.077 -    0.116: 109
       0.116 -    0.155: 12
       0.155 -    0.194: 4
  Chirality restraints: 2319
  Sorted by residual:
  chirality pdb=" C1'   U A  23 "
            pdb=" O4'   U A  23 "
            pdb=" C2'   U A  23 "
            pdb=" N1    U A  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.27    0.19 2.00e-01 2.50e+01 9.38e-01
  chirality pdb=" C1'   U A  66 "
            pdb=" O4'   U A  66 "
            pdb=" C2'   U A  66 "
            pdb=" N1    U A  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.29    0.18 2.00e-01 2.50e+01 7.81e-01
  chirality pdb=" C3'   C A  20 "
            pdb=" C4'   C A  20 "
            pdb=" O3'   C A  20 "
            pdb=" C2'   C A  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.64    0.17 2.00e-01 2.50e+01 6.83e-01
  ... (remaining 2316 not shown)

  Planarity restraints: 2088
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A  21 "   -0.009 2.00e-02 2.50e+03   1.41e-02 5.97e+00
        pdb=" N9    G A  21 "    0.004 2.00e-02 2.50e+03
        pdb=" C8    G A  21 "    0.019 2.00e-02 2.50e+03
        pdb=" N7    G A  21 "    0.018 2.00e-02 2.50e+03
        pdb=" C5    G A  21 "   -0.008 2.00e-02 2.50e+03
        pdb=" C6    G A  21 "   -0.009 2.00e-02 2.50e+03
        pdb=" O6    G A  21 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G A  21 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G A  21 "   -0.009 2.00e-02 2.50e+03
        pdb=" N2    G A  21 "    0.030 2.00e-02 2.50e+03
        pdb=" N3    G A  21 "   -0.011 2.00e-02 2.50e+03
        pdb=" C4    G A  21 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A  20 "   -0.024 2.00e-02 2.50e+03   1.47e-02 4.85e+00
        pdb=" N1    C A  20 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    C A  20 "    0.014 2.00e-02 2.50e+03
        pdb=" O2    C A  20 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    C A  20 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    C A  20 "    0.014 2.00e-02 2.50e+03
        pdb=" N4    C A  20 "   -0.028 2.00e-02 2.50e+03
        pdb=" C5    C A  20 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    C A  20 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U A  24 "   -0.023 2.00e-02 2.50e+03   1.30e-02 3.83e+00
        pdb=" N1    U A  24 "    0.031 2.00e-02 2.50e+03
        pdb=" C2    U A  24 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    U A  24 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    U A  24 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    U A  24 "   -0.006 2.00e-02 2.50e+03
        pdb=" O4    U A  24 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    U A  24 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U A  24 "    0.003 2.00e-02 2.50e+03
  ... (remaining 2085 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1078
        2.74 -     3.28: 13990
        3.28 -     3.82: 25029
        3.82 -     4.36: 29663
        4.36 -     4.90: 45961
  Nonbonded interactions: 115721
  Sorted by model distance:
  nonbonded pdb=" O2'   U A  59 "
            pdb=" OP1   C A  60 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OD1 ASP B1267 "
            pdb=" OH  TYR B1294 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   ALA B1227 "
            pdb=" N2    G A  89 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O2'   U A  56 "
            pdb=" N2    G A  58 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   LYS B 209 "
            pdb=" OG  SER B 213 "
     model   vdw
     2.252 3.040
  ... (remaining 115716 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 group one per residue
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:             3.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     15.250
  Find NCS groups from input model:        0.050
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
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   0.160  14623  Z= 0.198
  Angle     :  0.547   7.220  20341  Z= 0.329
  Chirality :  0.037   0.194   2319
  Planarity :  0.003   0.044   2088
  Dihedral  : 17.904 106.299   6294
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  5.02 %
    Favored  : 93.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.23), residues: 1353
  helix:  1.29 (0.21), residues: 667
  sheet: -0.28 (0.50), residues: 111
  loop : -0.33 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  78 
 TYR   0.007   0.001   TYR B1141 
 PHE   0.006   0.001   PHE B  97 
 TRP   0.005   0.001   TRP B 464 
 HIS   0.003   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (14623)
  covalent geometry    : angle       0.54703 (20341)
  hydrogen bonds       : bond        0.14878 (  640)
  hydrogen bonds       : angle       5.74630 ( 1727)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 194
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8124 (t0)
REVERT: B  139 ARG cc_start: 0.9032 (mtp180) cc_final: 0.8218 (mtp180)
REVERT: B  415 HIS cc_start: 0.8890 (m90) cc_final: 0.8268 (m-70)
REVERT: B  419 LEU cc_start: 0.9571 (tt) cc_final: 0.9349 (pp)
REVERT: B  534 MET cc_start: 0.4961 (mtp) cc_final: 0.3639 (ttp)
REVERT: B  659 TRP cc_start: 0.7501 (m100) cc_final: 0.6816 (m100)
REVERT: B  822 MET cc_start: 0.9514 (tpt) cc_final: 0.9082 (tpp)
REVERT: B  848 LYS cc_start: 0.5419 (OUTLIER) cc_final: 0.4142 (mptt)
REVERT: B  856 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.8813 (t)
REVERT: B  958 LEU cc_start: 0.9125 (mt) cc_final: 0.8606 (mt)
REVERT: B  966 PHE cc_start: 0.9123 (t80) cc_final: 0.8680 (t80)
REVERT: B 1213 MET cc_start: 0.7729 (mtm) cc_final: 0.6895 (ttm)
REVERT: B 1219 GLU cc_start: 0.8722 (tt0) cc_final: 0.8451 (tm-30)
REVERT: B 1355 LEU cc_start: 0.8630 (mt) cc_final: 0.8318 (mt)
  outliers start: 20
  outliers final: 5
  residues processed: 213
  average time/residue: 0.1519
  time to fit residues: 44.7539
Evaluate side-chains
  108 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    0.4980
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:    0.4980
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    0.3980
   overall best weight:    3.6784

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

Flipped N/Q/H residues before XYZ refinement:
B 113 HIS
B 129 HIS
B 341 GLN
B 369 GLN
B 412 HIS
B 415 HIS
B 459 ASN
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 612 ASN
** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 726 ASN
** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1297 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.061573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.046651 restraints weight = 118726.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.048036 restraints weight = 60339.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.048832 restraints weight = 39702.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.049330 restraints weight = 30954.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.049659 restraints weight = 26812.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14623  Z= 0.177
  Angle     :  0.542   8.136  20341  Z= 0.294
  Chirality :  0.037   0.165   2319
  Planarity :  0.004   0.053   2088
  Dihedral  : 20.886 107.864   3411
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.97 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.23), residues: 1353
  helix:  1.48 (0.20), residues: 683
  sheet:  0.27 (0.55), residues: 87
  loop : -0.13 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  78 
 TYR   0.015   0.001   TYR B1016 
 PHE   0.017   0.001   PHE B1313 
 TRP   0.011   0.001   TRP B 464 
 HIS   0.007   0.001   HIS B1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (14623)
  covalent geometry    : angle       0.54241 (20341)
  hydrogen bonds       : bond        0.04378 (  640)
  hydrogen bonds       : angle       4.57228 ( 1727)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  383 MET cc_start: 0.8657 (mmp) cc_final: 0.8091 (mmm)
REVERT: B  459 ASN cc_start: 0.4800 (OUTLIER) cc_final: 0.4302 (t0)
REVERT: B  534 MET cc_start: 0.4023 (mtp) cc_final: 0.2986 (ptp)
REVERT: B  659 TRP cc_start: 0.7935 (m100) cc_final: 0.7414 (m100)
REVERT: B  718 ASP cc_start: 0.9300 (m-30) cc_final: 0.8801 (p0)
REVERT: B  780 ARG cc_start: 0.9025 (mtt180) cc_final: 0.8668 (mtm-85)
REVERT: B  781 MET cc_start: 0.8952 (mmm) cc_final: 0.8440 (mmm)
REVERT: B  822 MET cc_start: 0.9568 (tpt) cc_final: 0.9247 (tpp)
REVERT: B 1094 ILE cc_start: 0.8431 (mm) cc_final: 0.8144 (tp)
REVERT: B 1095 VAL cc_start: 0.9538 (t) cc_final: 0.9182 (p)
REVERT: B 1213 MET cc_start: 0.7598 (mtm) cc_final: 0.7142 (ttm)
REVERT: B 1219 GLU cc_start: 0.8881 (tt0) cc_final: 0.8293 (tm-30)
REVERT: B 1350 GLN cc_start: 0.8923 (mt0) cc_final: 0.8655 (mm-40)
  outliers start: 1
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1177
  time to fit residues: 21.4164
Evaluate side-chains
  76 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 25 optimal weight:   20.0000
   chunk 118 optimal weight:   10.0000
   chunk 110 optimal weight:    8.9990
   chunk 83 optimal weight:   30.0000
   chunk 53 optimal weight:    0.6980
   chunk 137 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    5.1388

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

Flipped N/Q/H residues before XYZ refinement:
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 ASN
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 726 ASN
** B 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 863 ASN
** B1261 GLN ** 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 = 0.3596 r_free = 0.3596 target = 0.056642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.041479 restraints weight = 114141.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.042813 restraints weight = 59393.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.043565 restraints weight = 39779.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.044067 restraints weight = 31342.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.044384 restraints weight = 27130.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.3608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14623  Z= 0.217
  Angle     :  0.580   6.876  20341  Z= 0.314
  Chirality :  0.037   0.155   2319
  Planarity :  0.004   0.046   2088
  Dihedral  : 21.175 107.787   3411
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.23), residues: 1353
  helix:  1.47 (0.20), residues: 681
  sheet:  0.12 (0.62), residues: 72
  loop : -0.18 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  78 
 TYR   0.026   0.002   TYR B 136 
 PHE   0.020   0.002   PHE B 375 
 TRP   0.014   0.002   TRP B 464 
 HIS   0.005   0.001   HIS B1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (14623)
  covalent geometry    : angle       0.58042 (20341)
  hydrogen bonds       : bond        0.05257 (  640)
  hydrogen bonds       : angle       4.65325 ( 1727)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  161 MET cc_start: 0.9111 (tpp) cc_final: 0.8771 (mmm)
REVERT: B  383 MET cc_start: 0.8647 (mmp) cc_final: 0.8090 (mmm)
REVERT: B  534 MET cc_start: 0.3908 (mtp) cc_final: 0.2960 (ptp)
REVERT: B  718 ASP cc_start: 0.9351 (m-30) cc_final: 0.8881 (p0)
REVERT: B  740 THR cc_start: 0.8975 (m) cc_final: 0.8749 (m)
REVERT: B  780 ARG cc_start: 0.9047 (mtt180) cc_final: 0.8528 (mtm-85)
REVERT: B  781 MET cc_start: 0.9180 (mmm) cc_final: 0.8572 (mmm)
REVERT: B  794 GLN cc_start: 0.9663 (mm-40) cc_final: 0.9388 (mm-40)
REVERT: B  822 MET cc_start: 0.9592 (tpt) cc_final: 0.8701 (tpp)
REVERT: B  823 TYR cc_start: 0.8149 (m-10) cc_final: 0.7947 (m-10)
REVERT: B 1213 MET cc_start: 0.7626 (mtm) cc_final: 0.7074 (ttm)
REVERT: B 1219 GLU cc_start: 0.8925 (tt0) cc_final: 0.8214 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1168
  time to fit residues: 17.0545
Evaluate side-chains
  74 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 132 optimal weight:   10.0000
   chunk 88 optimal weight:   20.0000
   chunk 92 optimal weight:    7.9990
   chunk 26 optimal weight:   30.0000
   chunk 47 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 86 optimal weight:    7.9990
   chunk 83 optimal weight:    0.6980
   chunk 131 optimal weight:    0.8980
   overall best weight:    3.3186

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

Flipped N/Q/H residues before XYZ refinement:
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 726 ASN
B 899 ASN
** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.057069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.041325 restraints weight = 118614.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.042638 restraints weight = 65311.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.043369 restraints weight = 44976.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.043873 restraints weight = 36024.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.044218 restraints weight = 31339.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.3873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14623  Z= 0.150
  Angle     :  0.498   5.877  20341  Z= 0.272
  Chirality :  0.035   0.176   2319
  Planarity :  0.003   0.045   2088
  Dihedral  : 20.952 105.057   3411
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.23), residues: 1353
  helix:  1.63 (0.20), residues: 683
  sheet: -0.10 (0.66), residues: 64
  loop : -0.10 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  78 
 TYR   0.013   0.001   TYR B 136 
 PHE   0.014   0.001   PHE B 375 
 TRP   0.021   0.002   TRP B 464 
 HIS   0.004   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (14623)
  covalent geometry    : angle       0.49796 (20341)
  hydrogen bonds       : bond        0.04040 (  640)
  hydrogen bonds       : angle       4.39490 ( 1727)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  383 MET cc_start: 0.8668 (mmp) cc_final: 0.8101 (mmm)
REVERT: B  450 TYR cc_start: 0.6835 (m-80) cc_final: 0.6419 (m-10)
REVERT: B  534 MET cc_start: 0.4244 (mtp) cc_final: 0.3436 (ptp)
REVERT: B  718 ASP cc_start: 0.9385 (m-30) cc_final: 0.8826 (p0)
REVERT: B  722 GLU cc_start: 0.9535 (mp0) cc_final: 0.9026 (mp0)
REVERT: B  780 ARG cc_start: 0.8989 (mtt180) cc_final: 0.8537 (mtm-85)
REVERT: B  781 MET cc_start: 0.9257 (mmm) cc_final: 0.8673 (mmm)
REVERT: B  822 MET cc_start: 0.9554 (tpt) cc_final: 0.9115 (tpp)
REVERT: B 1213 MET cc_start: 0.7593 (mtm) cc_final: 0.7022 (ttm)
REVERT: B 1219 GLU cc_start: 0.8884 (tt0) cc_final: 0.8200 (tm-30)
REVERT: B 1242 TYR cc_start: 0.7874 (t80) cc_final: 0.7495 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1129
  time to fit residues: 17.1320
Evaluate side-chains
  74 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 145 optimal weight:   20.0000
   chunk 41 optimal weight:    7.9990
   chunk 137 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 132 optimal weight:   30.0000
   chunk 114 optimal weight:   20.0000
   chunk 25 optimal weight:   20.0000
   chunk 72 optimal weight:    3.9990
   chunk 141 optimal weight:   10.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 726 ASN
B 808 ASN
B 854 ASN
B 863 ASN
** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.054588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.039583 restraints weight = 122818.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.040852 restraints weight = 66003.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.041553 restraints weight = 44807.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.042032 restraints weight = 35584.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.042245 restraints weight = 31219.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.4566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  14623  Z= 0.252
  Angle     :  0.610   8.468  20341  Z= 0.328
  Chirality :  0.038   0.169   2319
  Planarity :  0.004   0.048   2088
  Dihedral  : 21.326 106.535   3411
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 17.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.56 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.23), residues: 1353
  helix:  1.39 (0.20), residues: 684
  sheet: -0.32 (0.61), residues: 74
  loop : -0.23 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 139 
 TYR   0.023   0.002   TYR B1265 
 PHE   0.017   0.002   PHE B 375 
 TRP   0.029   0.002   TRP B 464 
 HIS   0.005   0.001   HIS B 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 (14623)
  covalent geometry    : angle       0.61014 (20341)
  hydrogen bonds       : bond        0.05591 (  640)
  hydrogen bonds       : angle       4.72489 ( 1727)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  383 MET cc_start: 0.8674 (mmp) cc_final: 0.8040 (mmm)
REVERT: B  450 TYR cc_start: 0.6888 (m-80) cc_final: 0.6430 (m-80)
REVERT: B  534 MET cc_start: 0.4174 (mtp) cc_final: 0.3303 (ttp)
REVERT: B  718 ASP cc_start: 0.9373 (m-30) cc_final: 0.8867 (p0)
REVERT: B  722 GLU cc_start: 0.9511 (mp0) cc_final: 0.9105 (mp0)
REVERT: B  740 THR cc_start: 0.8978 (m) cc_final: 0.8724 (p)
REVERT: B  780 ARG cc_start: 0.8945 (mtt180) cc_final: 0.8432 (mtm-85)
REVERT: B  781 MET cc_start: 0.9262 (mmm) cc_final: 0.8665 (mmm)
REVERT: B 1213 MET cc_start: 0.7719 (mtm) cc_final: 0.7084 (ttm)
REVERT: B 1219 GLU cc_start: 0.8862 (tt0) cc_final: 0.8395 (tt0)
REVERT: B 1242 TYR cc_start: 0.8072 (t80) cc_final: 0.7689 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 87
  average time/residue: 0.1026
  time to fit residues: 13.6997
Evaluate side-chains
  63 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 89 optimal weight:   30.0000
   chunk 102 optimal weight:   20.0000
   chunk 47 optimal weight:    6.9990
   chunk 133 optimal weight:    5.9990
   chunk 76 optimal weight:   20.0000
   chunk 74 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   chunk 95 optimal weight:    8.9990
   chunk 62 optimal weight:   10.0000
   chunk 132 optimal weight:    5.9990
   chunk 20 optimal weight:   50.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 726 ASN
B 863 ASN
B 920 GLN
** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1264 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 = 0.3525 r_free = 0.3525 target = 0.054095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.038444 restraints weight = 123391.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.039757 restraints weight = 65219.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.040515 restraints weight = 44209.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.040984 restraints weight = 35188.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.041291 restraints weight = 30536.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.5059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  14623  Z= 0.246
  Angle     :  0.604   8.664  20341  Z= 0.328
  Chirality :  0.038   0.172   2319
  Planarity :  0.005   0.085   2088
  Dihedral  : 21.369 106.879   3411
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.23), residues: 1353
  helix:  1.24 (0.20), residues: 685
  sheet: -0.48 (0.61), residues: 74
  loop : -0.26 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  78 
 TYR   0.021   0.002   TYR B 128 
 PHE   0.015   0.002   PHE B 970 
 TRP   0.026   0.002   TRP B 464 
 HIS   0.006   0.001   HIS B 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 (14623)
  covalent geometry    : angle       0.60416 (20341)
  hydrogen bonds       : bond        0.05446 (  640)
  hydrogen bonds       : angle       4.84433 ( 1727)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  383 MET cc_start: 0.8768 (mmp) cc_final: 0.8088 (mmm)
REVERT: B  450 TYR cc_start: 0.7079 (m-80) cc_final: 0.6527 (m-80)
REVERT: B  534 MET cc_start: 0.4631 (mtp) cc_final: 0.4094 (ptm)
REVERT: B  659 TRP cc_start: 0.8482 (m100) cc_final: 0.8097 (m100)
REVERT: B  718 ASP cc_start: 0.9443 (m-30) cc_final: 0.8933 (p0)
REVERT: B  722 GLU cc_start: 0.9560 (mp0) cc_final: 0.9158 (mp0)
REVERT: B  781 MET cc_start: 0.9255 (mmm) cc_final: 0.8944 (mmm)
REVERT: B  822 MET cc_start: 0.9363 (mmp) cc_final: 0.8658 (mmm)
REVERT: B 1213 MET cc_start: 0.7745 (mtm) cc_final: 0.7154 (ttm)
REVERT: B 1219 GLU cc_start: 0.8787 (tt0) cc_final: 0.8095 (tm-30)
REVERT: B 1242 TYR cc_start: 0.8230 (t80) cc_final: 0.7857 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1098
  time to fit residues: 14.1500
Evaluate side-chains
  67 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 8 optimal weight:    9.9990
   chunk 111 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 124 optimal weight:    9.9990
   chunk 118 optimal weight:   10.0000
   chunk 123 optimal weight:   30.0000
   chunk 145 optimal weight:   20.0000
   chunk 26 optimal weight:   20.0000
   chunk 10 optimal weight:   10.0000
   overall best weight:    9.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 224 ASN
** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 863 ASN
** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.052061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.037173 restraints weight = 133652.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.038289 restraints weight = 74252.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.038894 restraints weight = 52097.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.039326 restraints weight = 42507.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.039593 restraints weight = 37573.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.5978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.104  14623  Z= 0.384
  Angle     :  0.800  12.587  20341  Z= 0.423
  Chirality :  0.044   0.242   2319
  Planarity :  0.006   0.081   2088
  Dihedral  : 21.987 109.590   3411
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 26.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.22), residues: 1353
  helix:  0.36 (0.19), residues: 691
  sheet: -0.77 (0.57), residues: 80
  loop : -0.59 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  71 
 TYR   0.030   0.003   TYR B 450 
 PHE   0.025   0.003   PHE B1204 
 TRP   0.038   0.003   TRP B 464 
 HIS   0.010   0.002   HIS B1264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00779 (14623)
  covalent geometry    : angle       0.80016 (20341)
  hydrogen bonds       : bond        0.07748 (  640)
  hydrogen bonds       : angle       5.55790 ( 1727)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  383 MET cc_start: 0.8699 (mmp) cc_final: 0.8043 (mmm)
REVERT: B  534 MET cc_start: 0.4356 (mtp) cc_final: 0.3878 (ttp)
REVERT: B  659 TRP cc_start: 0.8568 (m100) cc_final: 0.8151 (m100)
REVERT: B  718 ASP cc_start: 0.9494 (m-30) cc_final: 0.9069 (p0)
REVERT: B  763 MET cc_start: 0.8161 (tpt) cc_final: 0.7698 (tpt)
REVERT: B  781 MET cc_start: 0.9235 (mmm) cc_final: 0.8906 (mmm)
REVERT: B  822 MET cc_start: 0.9207 (mmp) cc_final: 0.8688 (mmm)
REVERT: B  823 TYR cc_start: 0.8787 (m-10) cc_final: 0.8569 (m-10)
REVERT: B 1043 MET cc_start: 0.9157 (tpt) cc_final: 0.8744 (tpt)
REVERT: B 1242 TYR cc_start: 0.8334 (t80) cc_final: 0.7978 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0987
  time to fit residues: 10.5143
Evaluate side-chains
  51 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 135 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 89 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 145 optimal weight:   10.0000
   chunk 117 optimal weight:    1.9990
   chunk 69 optimal weight:   30.0000
   chunk 93 optimal weight:    4.9990
   chunk 109 optimal weight:    0.5980
   chunk 54 optimal weight:    8.9990
   chunk 125 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B 224 ASN
B 281 GLN
B 726 ASN
** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1261 GLN ** 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 = 0.3565 r_free = 0.3565 target = 0.055641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.040503 restraints weight = 121215.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.041761 restraints weight = 65110.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.042478 restraints weight = 44650.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.042985 restraints weight = 35821.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.043210 restraints weight = 31232.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.5586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  14623  Z= 0.119
  Angle     :  0.531   9.600  20341  Z= 0.287
  Chirality :  0.036   0.184   2319
  Planarity :  0.004   0.046   2088
  Dihedral  : 21.114 103.943   3411
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.23), residues: 1353
  helix:  1.34 (0.20), residues: 692
  sheet: -0.44 (0.59), residues: 75
  loop : -0.29 (0.27), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B1122 
 TYR   0.018   0.001   TYR B1265 
 PHE   0.012   0.001   PHE B 375 
 TRP   0.029   0.002   TRP B 464 
 HIS   0.005   0.001   HIS B 721 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (14623)
  covalent geometry    : angle       0.53068 (20341)
  hydrogen bonds       : bond        0.03758 (  640)
  hydrogen bonds       : angle       4.62308 ( 1727)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  174 LEU cc_start: 0.9223 (pp) cc_final: 0.8790 (mp)
REVERT: B  383 MET cc_start: 0.8714 (mmp) cc_final: 0.7930 (mmm)
REVERT: B  450 TYR cc_start: 0.6990 (m-80) cc_final: 0.6479 (m-10)
REVERT: B  534 MET cc_start: 0.4123 (mtp) cc_final: 0.3829 (ptm)
REVERT: B  659 TRP cc_start: 0.8545 (m100) cc_final: 0.8020 (m100)
REVERT: B  718 ASP cc_start: 0.9512 (m-30) cc_final: 0.9047 (p0)
REVERT: B  722 GLU cc_start: 0.9516 (mp0) cc_final: 0.9197 (mp0)
REVERT: B  763 MET cc_start: 0.8404 (tpt) cc_final: 0.8116 (tpp)
REVERT: B  781 MET cc_start: 0.9205 (mmm) cc_final: 0.8893 (mmm)
REVERT: B  822 MET cc_start: 0.9334 (mmp) cc_final: 0.8762 (mmm)
REVERT: B 1042 ILE cc_start: 0.9276 (pt) cc_final: 0.9073 (pt)
REVERT: B 1043 MET cc_start: 0.9172 (tpt) cc_final: 0.8905 (tpt)
REVERT: B 1044 ASN cc_start: 0.9180 (m110) cc_final: 0.8519 (t0)
REVERT: B 1169 MET cc_start: 0.8111 (mmp) cc_final: 0.7820 (mmp)
REVERT: B 1242 TYR cc_start: 0.8078 (t80) cc_final: 0.7662 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.1213
  time to fit residues: 15.9531
Evaluate side-chains
  66 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 133 optimal weight:   20.0000
   chunk 85 optimal weight:   40.0000
   chunk 124 optimal weight:    9.9990
   chunk 136 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 68 optimal weight:    7.9990
   chunk 107 optimal weight:   10.0000
   chunk 32 optimal weight:    8.9990
   chunk 123 optimal weight:    9.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 726 ASN
B 863 ASN
** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1221 GLN
B1261 GLN
** B1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.052939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.038068 restraints weight = 129276.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.039238 restraints weight = 71006.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.039880 restraints weight = 49333.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.040281 restraints weight = 39900.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.040576 restraints weight = 35420.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.6024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083  14623  Z= 0.273
  Angle     :  0.664  12.116  20341  Z= 0.351
  Chirality :  0.039   0.196   2319
  Planarity :  0.005   0.066   2088
  Dihedral  : 21.474 107.637   3411
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 19.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.41 (0.23), residues: 1353
  helix:  1.01 (0.20), residues: 690
  sheet: -0.43 (0.59), residues: 80
  loop : -0.44 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  70 
 TYR   0.024   0.002   TYR B1265 
 PHE   0.017   0.002   PHE B 375 
 TRP   0.048   0.003   TRP B 464 
 HIS   0.008   0.002   HIS B1262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 (14623)
  covalent geometry    : angle       0.66355 (20341)
  hydrogen bonds       : bond        0.06053 (  640)
  hydrogen bonds       : angle       5.09959 ( 1727)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  383 MET cc_start: 0.8692 (mmp) cc_final: 0.7984 (mmm)
REVERT: B  534 MET cc_start: 0.4103 (mtp) cc_final: 0.3572 (ttp)
REVERT: B  659 TRP cc_start: 0.8600 (m100) cc_final: 0.8116 (m100)
REVERT: B  718 ASP cc_start: 0.9533 (m-30) cc_final: 0.9072 (p0)
REVERT: B  722 GLU cc_start: 0.9504 (mp0) cc_final: 0.9138 (mp0)
REVERT: B  763 MET cc_start: 0.8288 (tpt) cc_final: 0.8009 (tpp)
REVERT: B  781 MET cc_start: 0.9208 (mmm) cc_final: 0.8866 (mmm)
REVERT: B  822 MET cc_start: 0.9327 (mmp) cc_final: 0.8849 (mmm)
REVERT: B 1169 MET cc_start: 0.8131 (mmp) cc_final: 0.7290 (ttt)
REVERT: B 1219 GLU cc_start: 0.8891 (tt0) cc_final: 0.8252 (tm-30)
REVERT: B 1242 TYR cc_start: 0.8164 (t80) cc_final: 0.7828 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1052
  time to fit residues: 11.7535
Evaluate side-chains
  53 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 119 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 85 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 141 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 93 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0070
   overall best weight:    3.2006

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

Flipped N/Q/H residues before XYZ refinement:
B 726 ASN
B 863 ASN
** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.054523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.039627 restraints weight = 125758.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.040863 restraints weight = 69212.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.041588 restraints weight = 47903.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.041994 restraints weight = 38276.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.042285 restraints weight = 33764.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.5990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14623  Z= 0.155
  Angle     :  0.557  10.534  20341  Z= 0.295
  Chirality :  0.036   0.174   2319
  Planarity :  0.004   0.049   2088
  Dihedral  : 21.150 105.287   3411
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.23), residues: 1353
  helix:  1.34 (0.20), residues: 691
  sheet:  0.02 (0.71), residues: 54
  loop : -0.41 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 753 
 TYR   0.018   0.001   TYR B1265 
 PHE   0.013   0.001   PHE B 375 
 TRP   0.027   0.002   TRP B 464 
 HIS   0.006   0.001   HIS B 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (14623)
  covalent geometry    : angle       0.55729 (20341)
  hydrogen bonds       : bond        0.04200 (  640)
  hydrogen bonds       : angle       4.75815 ( 1727)

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

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

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2706 Ramachandran restraints generated.
    1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  383 MET cc_start: 0.8680 (mmp) cc_final: 0.7945 (mmm)
REVERT: B  450 TYR cc_start: 0.7043 (m-80) cc_final: 0.6531 (m-10)
REVERT: B  659 TRP cc_start: 0.8607 (m100) cc_final: 0.8123 (m100)
REVERT: B  718 ASP cc_start: 0.9553 (m-30) cc_final: 0.9145 (p0)
REVERT: B  722 GLU cc_start: 0.9495 (mp0) cc_final: 0.9200 (mp0)
REVERT: B  763 MET cc_start: 0.8404 (tpt) cc_final: 0.8119 (tpp)
REVERT: B  781 MET cc_start: 0.9186 (mmm) cc_final: 0.8845 (mmm)
REVERT: B  822 MET cc_start: 0.9331 (mmp) cc_final: 0.8856 (mmm)
REVERT: B 1042 ILE cc_start: 0.9285 (pt) cc_final: 0.9056 (pt)
REVERT: B 1043 MET cc_start: 0.9112 (tpt) cc_final: 0.8892 (tpt)
REVERT: B 1044 ASN cc_start: 0.9200 (m110) cc_final: 0.8502 (t0)
REVERT: B 1169 MET cc_start: 0.7993 (mmp) cc_final: 0.7213 (ttt)
REVERT: B 1219 GLU cc_start: 0.8847 (tt0) cc_final: 0.8089 (tp30)
REVERT: B 1242 TYR cc_start: 0.8097 (t80) cc_final: 0.7707 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1031
  time to fit residues: 13.0734
Evaluate side-chains
  64 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 17 optimal weight:   30.0000
   chunk 133 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   chunk 112 optimal weight:    3.9990
   chunk 58 optimal weight:   50.0000
   chunk 55 optimal weight:   30.0000
   chunk 33 optimal weight:    9.9990
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   chunk 89 optimal weight:   40.0000
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
B 726 ASN
B 863 ASN
** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.054628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.039794 restraints weight = 124264.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.040995 restraints weight = 68854.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.041737 restraints weight = 47787.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.042015 restraints weight = 38286.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.042431 restraints weight = 34382.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.6063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14623  Z= 0.145
  Angle     :  0.538  11.005  20341  Z= 0.285
  Chirality :  0.036   0.176   2319
  Planarity :  0.004   0.050   2088
  Dihedral  : 21.042 104.797   3411
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.08 %
    Favored  : 99.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.82 (0.23), residues: 1353
  helix:  1.44 (0.20), residues: 693
  sheet: -0.36 (0.63), residues: 71
  loop : -0.36 (0.27), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1122 
 TYR   0.017   0.001   TYR B   5 
 PHE   0.011   0.001   PHE B 375 
 TRP   0.027   0.002   TRP B 464 
 HIS   0.006   0.001   HIS B 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (14623)
  covalent geometry    : angle       0.53836 (20341)
  hydrogen bonds       : bond        0.04055 (  640)
  hydrogen bonds       : angle       4.61906 ( 1727)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2695.03 seconds
wall clock time: 47 minutes 14.48 seconds (2834.48 seconds total)