Starting phenix.real_space_refine
on Sat Oct 11 11:14:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sqh_40705/10_2025/8sqh_40705.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sqh_40705/10_2025/8sqh_40705.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sqh_40705/10_2025/8sqh_40705.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sqh_40705/10_2025/8sqh_40705.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sqh_40705/10_2025/8sqh_40705.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sqh_40705/10_2025/8sqh_40705.cif"
  }
  resolution = 3.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P     146      5.49       5
     Mg      4      5.21       5
     S      22      5.16       5
     C    8430      2.51       5
     N    2476      2.21       5
     O    3023      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14101
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 11002
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1341, 11002
          Classifications: {'peptide': 1341}
          Link IDs: {'PTRANS': 36, 'TRANS': 1304}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2100
          Classifications: {'RNA': 98}
          Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 52, 'rna3p_pyr': 34}
          Link IDs: {'rna2p': 11, 'rna3p': 86}
    Chain: "C"
      Number of atoms: 269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 269
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
    Chain: "D"
      Number of atoms: 342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 342
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
          Chain breaks: 1
    Chain: "c"
      Number of atoms: 384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 384
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.54, per 1000 atoms: 0.25
  Number of scatterers: 14101
  At special positions: 0
  Unit cell: (85.54, 119.38, 130.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      22     16.00
     P     146     15.00
     Mg      4     11.99
     O    3023      8.00
     N    2476      7.00
     C    8430      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: 1.19
  Conformation dependent library (CDL) restraints added in 519.3 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2554

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 11 sheets defined
      53.8% alpha, 10.0% beta
      54 base pairs and 82 stacking pairs defined.
    Time for finding SS restraints: 2.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 4.997A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.278A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.568A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 184 through 196
    Processing helix  chain 'A' and resid 208 through 213
    Processing helix  chain 'A' and resid 217 through 229
      removed outlier: 4.607A  pdb=" N   GLU A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 306
    Processing helix  chain 'A' and resid 315 through 343
    Processing helix  chain 'A' and resid 346 through 352
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 383
      Proline residue:  A 378  - end of helix
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.510A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.371A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.807A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 483 through 494
      removed outlier: 3.738A  pdb=" N   ILE A 492 " --> pdb=" O   ALA A 488 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG A 494 " --> pdb=" O   SER A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 525
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 553 through 556
      removed outlier: 3.623A  pdb=" N   ASN A 556 " --> pdb=" O   PHE A 553 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 553 through 556'
    Processing helix  chain 'A' and resid 560 through 568
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 603 through 609
    Processing helix  chain 'A' and resid 612 through 626
      removed outlier: 3.600A  pdb=" N   LEU A 616 " --> pdb=" O   ASN A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 642
      removed outlier: 4.397A  pdb=" N   HIS A 641 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 652
    Processing helix  chain 'A' and resid 663 through 668
      removed outlier: 3.550A  pdb=" N   ILE A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 699
    Processing helix  chain 'A' and resid 703 through 712
      removed outlier: 3.844A  pdb=" N   ASP A 707 " --> pdb=" O   THR A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 726
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 4.354A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   LYS A 735 " --> pdb=" O   PRO A 731 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   GLY A 736 " --> pdb=" O   ALA A 732 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   MET A 751 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 777
    Processing helix  chain 'A' and resid 779 through 792
      removed outlier: 3.603A  pdb=" N   ARG A 783 " --> pdb=" O   GLU A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 799
    Processing helix  chain 'A' and resid 802 through 807
      removed outlier: 3.717A  pdb=" N   GLN A 805 " --> pdb=" O   GLU A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 817
    Processing helix  chain 'A' and resid 851 through 853
      No H-bonds generated for 'chain 'A' and resid 851 through 853'
    Processing helix  chain 'A' and resid 859 through 866
    Processing helix  chain 'A' and resid 872 through 888
      removed outlier: 5.679A  pdb=" N   ASN A 881 " --> pdb=" O   LYS A 877 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   TYR A 882 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 901
    Processing helix  chain 'A' and resid 902 through 906
    Processing helix  chain 'A' and resid 909 through 913
    Processing helix  chain 'A' and resid 917 through 940
      removed outlier: 4.142A  pdb=" N   LEU A 921 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 970
    Processing helix  chain 'A' and resid 980 through 1001
      removed outlier: 4.398A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1009
      removed outlier: 3.652A  pdb=" N   PHE A1008 " --> pdb=" O   LEU A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1030 through 1042
    Processing helix  chain 'A' and resid 1043 through 1047
    Processing helix  chain 'A' and resid 1077 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1168 through 1177
      removed outlier: 4.377A  pdb=" N   SER A1172 " --> pdb=" O   ILE A1168 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   SER A1173 " --> pdb=" O   MET A1169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1191 through 1195
      removed outlier: 3.519A  pdb=" N   LEU A1194 " --> pdb=" O   LYS A1191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1240
    Processing helix  chain 'A' and resid 1248 through 1262
    Processing helix  chain 'A' and resid 1264 through 1281
    Processing helix  chain 'A' and resid 1283 through 1298
    Processing helix  chain 'A' and resid 1301 through 1313
    Processing helix  chain 'A' and resid 1314 through 1316
      No H-bonds generated for 'chain 'A' and resid 1314 through 1316'
    Processing helix  chain 'A' and resid 1340 through 1344
      removed outlier: 4.148A  pdb=" N   ASP A1344 " --> pdb=" O   GLU A1341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959
      removed outlier: 6.290A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   LEU A 958 " --> pdb=" O   ILE A 759 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   ILE A 761 " --> pdb=" O   LEU A 958 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   GLU A 762 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 7.820A  pdb=" N   LEU A   9 " --> pdb=" O   GLU A 762 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46
      removed outlier: 4.587A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   GLN A1219 " --> pdb=" O   ALA A1215 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 253
      removed outlier: 3.904A  pdb=" N   PHE A 252 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA5, first strand: chain 'A' and resid 837 through 840
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1049 through 1051
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1063 through 1065
      removed outlier: 3.702A  pdb=" N   TRP A1074 " --> pdb=" O   GLU A1064 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1120 through 1121
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1156 through 1167
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.752A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1324 through 1326

    515 hydrogen bonds defined for protein.
    1467 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      133 hydrogen bonds
      262 hydrogen bond angles
      0 basepair planarities
      54 basepair parallelities
      82 stacking parallelities
  Total time for adding SS restraints: 3.83

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3719
        1.34 -     1.46: 3699
        1.46 -     1.58: 6914
        1.58 -     1.70: 286
        1.70 -     1.82: 42
  Bond restraints: 14660
  Sorted by residual:
  bond pdb=" CA  ASP A 585 "
       pdb=" CB  ASP A 585 "
    ideal  model  delta    sigma   weight residual
    1.530  1.567 -0.037 1.69e-02 3.50e+03 4.68e+00
  bond pdb=" O5'  DG c  12 "
       pdb=" C5'  DG c  12 "
    ideal  model  delta    sigma   weight residual
    1.423  1.360  0.063 3.00e-02 1.11e+03 4.38e+00
  bond pdb=" O5'  DT c   9 "
       pdb=" C5'  DT c   9 "
    ideal  model  delta    sigma   weight residual
    1.423  1.363  0.060 3.00e-02 1.11e+03 4.02e+00
  bond pdb=" C1'  DC c   6 "
       pdb=" N1   DC c   6 "
    ideal  model  delta    sigma   weight residual
    1.490  1.550 -0.060 3.00e-02 1.11e+03 4.01e+00
  bond pdb=" CB  PRO A 800 "
       pdb=" CG  PRO A 800 "
    ideal  model  delta    sigma   weight residual
    1.492  1.588 -0.096 5.00e-02 4.00e+02 3.68e+00
  ... (remaining 14655 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.94: 19846
        2.94 -     5.88: 462
        5.88 -     8.82: 77
        8.82 -    11.76: 18
       11.76 -    14.70: 7
  Bond angle restraints: 20410
  Sorted by residual:
  angle pdb=" O3'   G B  11 "
        pdb=" C3'   G B  11 "
        pdb=" C2'   G B  11 "
      ideal   model   delta    sigma   weight residual
     113.70  122.01   -8.31 1.50e+00 4.44e-01 3.07e+01
  angle pdb=" CB  LYS A1158 "
        pdb=" CG  LYS A1158 "
        pdb=" CD  LYS A1158 "
      ideal   model   delta    sigma   weight residual
     111.30  123.40  -12.10 2.30e+00 1.89e-01 2.77e+01
  angle pdb=" CA  ASP A 585 "
        pdb=" CB  ASP A 585 "
        pdb=" CG  ASP A 585 "
      ideal   model   delta    sigma   weight residual
     112.60  117.73   -5.13 1.00e+00 1.00e+00 2.63e+01
  angle pdb=" C2'   A B   8 "
        pdb=" C1'   A B   8 "
        pdb=" N9    A B   8 "
      ideal   model   delta    sigma   weight residual
     112.00  119.70   -7.70 1.50e+00 4.44e-01 2.63e+01
  angle pdb=" CB  LYS A 775 "
        pdb=" CG  LYS A 775 "
        pdb=" CD  LYS A 775 "
      ideal   model   delta    sigma   weight residual
     111.30  123.03  -11.73 2.30e+00 1.89e-01 2.60e+01
  ... (remaining 20405 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.86: 8202
       29.86 -    59.71: 571
       59.71 -    89.57: 115
       89.57 -   119.42: 3
      119.42 -   149.28: 2
  Dihedral angle restraints: 8893
    sinusoidal: 4949
      harmonic: 3944
  Sorted by residual:
  dihedral pdb=" CA  SER A1106 "
           pdb=" C   SER A1106 "
           pdb=" N   LYS A1107 "
           pdb=" CA  LYS A1107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.05   27.95     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  ASP A 837 "
           pdb=" C   ASP A 837 "
           pdb=" N   VAL A 838 "
           pdb=" CA  VAL A 838 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.89   27.11     0      5.00e+00 4.00e-02 2.94e+01
  dihedral pdb=" CA  LYS A 526 "
           pdb=" C   LYS A 526 "
           pdb=" N   VAL A 527 "
           pdb=" CA  VAL A 527 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.40   26.60     0      5.00e+00 4.00e-02 2.83e+01
  ... (remaining 8890 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.127: 2235
       0.127 -    0.255: 87
       0.255 -    0.382: 10
       0.382 -    0.510: 1
       0.510 -    0.637: 4
  Chirality restraints: 2337
  Sorted by residual:
  chirality pdb=" C3'   A B  12 "
            pdb=" C4'   A B  12 "
            pdb=" O3'   A B  12 "
            pdb=" C2'   A B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.84   -0.64 2.00e-01 2.50e+01 1.01e+01
  chirality pdb=" C4'   A B  12 "
            pdb=" C5'   A B  12 "
            pdb=" O4'   A B  12 "
            pdb=" C3'   A B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -1.86   -0.63 2.00e-01 2.50e+01 1.01e+01
  chirality pdb=" C3'   G B  11 "
            pdb=" C4'   G B  11 "
            pdb=" O3'   G B  11 "
            pdb=" C2'   G B  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.89   -0.59 2.00e-01 2.50e+01 8.57e+00
  ... (remaining 2334 not shown)

  Planarity restraints: 2074
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG D  41 "   -0.063 2.00e-02 2.50e+03   2.90e-02 2.53e+01
        pdb=" N9   DG D  41 "    0.075 2.00e-02 2.50e+03
        pdb=" C8   DG D  41 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DG D  41 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DG D  41 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DG D  41 "   -0.006 2.00e-02 2.50e+03
        pdb=" O6   DG D  41 "   -0.015 2.00e-02 2.50e+03
        pdb=" N1   DG D  41 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2   DG D  41 "    0.001 2.00e-02 2.50e+03
        pdb=" N2   DG D  41 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DG D  41 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DG D  41 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   1 "    0.040 2.00e-02 2.50e+03   2.88e-02 2.49e+01
        pdb=" N9    G B   1 "   -0.084 2.00e-02 2.50e+03
        pdb=" C8    G B   1 "    0.005 2.00e-02 2.50e+03
        pdb=" N7    G B   1 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    G B   1 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G B   1 "    0.008 2.00e-02 2.50e+03
        pdb=" O6    G B   1 "    0.001 2.00e-02 2.50e+03
        pdb=" N1    G B   1 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G B   1 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2    G B   1 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3    G B   1 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G B   1 "    0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT c  11 "    0.026 2.00e-02 2.50e+03   2.94e-02 2.16e+01
        pdb=" N1   DT c  11 "   -0.074 2.00e-02 2.50e+03
        pdb=" C2   DT c  11 "    0.047 2.00e-02 2.50e+03
        pdb=" O2   DT c  11 "   -0.007 2.00e-02 2.50e+03
        pdb=" N3   DT c  11 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4   DT c  11 "   -0.001 2.00e-02 2.50e+03
        pdb=" O4   DT c  11 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DT c  11 "    0.005 2.00e-02 2.50e+03
        pdb=" C7   DT c  11 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DT c  11 "    0.006 2.00e-02 2.50e+03
  ... (remaining 2071 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 79
        2.54 -     3.13: 10533
        3.13 -     3.72: 24467
        3.72 -     4.31: 32720
        4.31 -     4.90: 50396
  Nonbonded interactions: 118195
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  10 "
            pdb="MG    MG A1402 "
     model   vdw
     1.955 2.170
  nonbonded pdb=" OP1  DC D  34 "
            pdb="MG    MG A1401 "
     model   vdw
     2.015 2.170
  nonbonded pdb=" ND1 HIS A 983 "
            pdb="MG    MG A1402 "
     model   vdw
     2.040 2.250
  nonbonded pdb=" OE1 GLU A 762 "
            pdb="MG    MG A1401 "
     model   vdw
     2.045 2.170
  nonbonded pdb=" OP2   A B  65 "
            pdb="MG    MG B 101 "
     model   vdw
     2.062 2.170
  ... (remaining 118190 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             4.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.000
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:1.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.096  14660  Z= 0.250
  Angle     :  1.119  14.698  20410  Z= 0.609
  Chirality :  0.064   0.637   2337
  Planarity :  0.008   0.083   2074
  Dihedral  : 19.150 149.280   6339
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  : 17.78 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.08 %
  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 aren not related in a simple way.
  whole: -1.51 (0.21), residues: 1333
  helix: -1.07 (0.18), residues: 629
  sheet: -0.29 (0.64), residues: 80
  loop : -0.86 (0.23), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.039   0.003   ARG A 220 
 TYR   0.033   0.004   TYR A 192 
 PHE   0.033   0.002   PHE A1046 
 TRP   0.031   0.003   TRP A1136 
 HIS   0.010   0.002   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 (14660)
  covalent geometry    : angle       1.11930 (20410)
  hydrogen bonds       : bond        0.13845 (  636)
  hydrogen bonds       : angle       6.07353 ( 1729)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1325 LYS cc_start: 0.9228 (ptmt) cc_final: 0.8750 (ttpp)
  outliers start: 2
  outliers final: 1
  residues processed: 51
  average time/residue: 0.1437
  time to fit residues: 10.9405
Evaluate side-chains
  42 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  921 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.043804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.032984 restraints weight = 91306.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.034049 restraints weight = 43655.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.034752 restraints weight = 28361.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.035171 restraints weight = 21752.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.035394 restraints weight = 18537.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14660  Z= 0.202
  Angle     :  0.625   8.805  20410  Z= 0.334
  Chirality :  0.039   0.221   2337
  Planarity :  0.004   0.044   2074
  Dihedral  : 19.532 157.081   3465
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 13.90 %
    Favored  : 83.79 %
  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 aren not related in a simple way.
  whole: -0.03 (0.23), residues: 1333
  helix:  0.30 (0.20), residues: 643
  sheet:  0.04 (0.51), residues: 106
  loop : -0.22 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 859 
 TYR   0.022   0.001   TYR A 192 
 PHE   0.012   0.001   PHE A 432 
 TRP   0.019   0.002   TRP A1136 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (14660)
  covalent geometry    : angle       0.62537 (20410)
  hydrogen bonds       : bond        0.04531 (  636)
  hydrogen bonds       : angle       4.73909 ( 1729)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 45
  time to evaluate  : 0.373 
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: A  196 PHE cc_start: 0.9650 (t80) cc_final: 0.9438 (t80)
REVERT: A  647 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9135 (m)
REVERT: A  974 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8891 (ptmt)
  outliers start: 28
  outliers final: 8
  residues processed: 72
  average time/residue: 0.1443
  time to fit residues: 14.9458
Evaluate side-chains
  50 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  837 ASP
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue 1006 SER
Chi-restraints excluded: chain A residue 1156 LYS
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1328 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 143 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 126 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 92 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 202 ASN
A1208 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.042372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.031575 restraints weight = 93032.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.032634 restraints weight = 44323.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.033311 restraints weight = 28710.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.033737 restraints weight = 22109.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.033955 restraints weight = 18854.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  14660  Z= 0.194
  Angle     :  0.578  12.564  20410  Z= 0.307
  Chirality :  0.038   0.184   2337
  Planarity :  0.003   0.045   2074
  Dihedral  : 19.481 156.569   3465
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.64 %
    Favored  : 82.96 %
  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 aren not related in a simple way.
  whole:  0.47 (0.23), residues: 1333
  helix:  0.72 (0.20), residues: 643
  sheet:  0.21 (0.52), residues: 106
  loop :  0.02 (0.27), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 951 
 TYR   0.018   0.001   TYR A 192 
 PHE   0.010   0.001   PHE A 575 
 TRP   0.012   0.001   TRP A1136 
 HIS   0.010   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (14660)
  covalent geometry    : angle       0.57773 (20410)
  hydrogen bonds       : bond        0.04181 (  636)
  hydrogen bonds       : angle       4.44743 ( 1729)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 43
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 PHE cc_start: 0.9672 (t80) cc_final: 0.9463 (t80)
REVERT: A  585 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8272 (p0)
REVERT: A  807 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8857 (mp10)
REVERT: A  974 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8823 (ptmt)
REVERT: A 1325 LYS cc_start: 0.9319 (ptmt) cc_final: 0.9054 (tttm)
  outliers start: 29
  outliers final: 10
  residues processed: 71
  average time/residue: 0.1415
  time to fit residues: 14.7126
Evaluate side-chains
  53 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  585 ASP
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue 1006 SER
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1156 LYS
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1360 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 129 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   chunk 102 optimal weight:    0.0980
   chunk 135 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 29 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 134 optimal weight:    6.9990
   chunk 128 optimal weight:    3.9990
   chunk 76 optimal weight:    7.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1208 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.041825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.031095 restraints weight = 94181.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.032116 restraints weight = 44519.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.032779 restraints weight = 28788.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.033185 restraints weight = 22215.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.033455 restraints weight = 19055.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14660  Z= 0.193
  Angle     :  0.567  11.864  20410  Z= 0.298
  Chirality :  0.037   0.179   2337
  Planarity :  0.003   0.044   2074
  Dihedral  : 19.407 157.865   3465
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.22 %
    Favored  : 82.46 %
  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 aren not related in a simple way.
  whole:  0.61 (0.23), residues: 1333
  helix:  0.92 (0.20), residues: 644
  sheet:  0.21 (0.52), residues: 104
  loop : -0.01 (0.27), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 832 
 TYR   0.015   0.001   TYR A 155 
 PHE   0.012   0.001   PHE A 575 
 TRP   0.010   0.001   TRP A1136 
 HIS   0.008   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (14660)
  covalent geometry    : angle       0.56658 (20410)
  hydrogen bonds       : bond        0.04033 (  636)
  hydrogen bonds       : angle       4.32921 ( 1729)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 42
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 PHE cc_start: 0.9661 (t80) cc_final: 0.9432 (t80)
REVERT: A  294 LYS cc_start: 0.9201 (tmtt) cc_final: 0.8887 (tmtt)
REVERT: A  804 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8712 (t)
REVERT: A  974 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8769 (ptmt)
REVERT: A 1006 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8661 (t)
  outliers start: 28
  outliers final: 13
  residues processed: 67
  average time/residue: 0.1375
  time to fit residues: 13.5507
Evaluate side-chains
  56 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 40
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  804 THR
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue  975 VAL
Chi-restraints excluded: chain A residue 1006 SER
Chi-restraints excluded: chain A residue 1014 LYS
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1156 LYS
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1360 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 107 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 131 optimal weight:    0.0770
   chunk 145 optimal weight:    4.9990
   chunk 111 optimal weight:    3.9990
   chunk 122 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   overall best weight:    1.1942

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 HIS
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.042479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.031852 restraints weight = 92228.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.032908 restraints weight = 42992.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.033595 restraints weight = 27548.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.033986 restraints weight = 21069.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.034252 restraints weight = 18118.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8713
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14660  Z= 0.129
  Angle     :  0.523  11.663  20410  Z= 0.277
  Chirality :  0.036   0.182   2337
  Planarity :  0.003   0.043   2074
  Dihedral  : 19.339 155.448   3465
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.85 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 15.80 %
    Favored  : 82.30 %
  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 aren not related in a simple way.
  whole:  0.75 (0.24), residues: 1333
  helix:  1.11 (0.21), residues: 639
  sheet:  0.28 (0.52), residues: 106
  loop : -0.02 (0.27), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 220 
 TYR   0.015   0.001   TYR A 192 
 PHE   0.010   0.001   PHE A 575 
 TRP   0.005   0.001   TRP A1136 
 HIS   0.007   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (14660)
  covalent geometry    : angle       0.52290 (20410)
  hydrogen bonds       : bond        0.03582 (  636)
  hydrogen bonds       : angle       4.18224 ( 1729)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 43
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 PHE cc_start: 0.9655 (t80) cc_final: 0.9453 (t80)
REVERT: A  261 ASP cc_start: 0.0661 (OUTLIER) cc_final: -0.0523 (t0)
REVERT: A  294 LYS cc_start: 0.9252 (tmtt) cc_final: 0.8941 (tmtt)
REVERT: A  495 MET cc_start: 0.9091 (ttm) cc_final: 0.8843 (ttm)
REVERT: A  664 ARG cc_start: 0.9399 (OUTLIER) cc_final: 0.8961 (tmm-80)
REVERT: A  763 MET cc_start: 0.9197 (tpp) cc_final: 0.8886 (tpp)
REVERT: A  974 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8748 (ptmt)
REVERT: A 1006 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8650 (t)
REVERT: A 1325 LYS cc_start: 0.9293 (ptmt) cc_final: 0.9018 (tttt)
  outliers start: 23
  outliers final: 13
  residues processed: 63
  average time/residue: 0.1390
  time to fit residues: 12.9888
Evaluate side-chains
  58 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 41
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  664 ARG
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  837 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue 1006 SER
Chi-restraints excluded: chain A residue 1089 MET
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1156 LYS
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1360 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 125 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 97 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 25 optimal weight:   20.0000
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 HIS
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.040786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.030175 restraints weight = 96065.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.031171 restraints weight = 45796.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.031808 restraints weight = 29659.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.032210 restraints weight = 22932.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.032399 restraints weight = 19668.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8770
moved from start:          0.3029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  14660  Z= 0.260
  Angle     :  0.613   9.641  20410  Z= 0.321
  Chirality :  0.038   0.177   2337
  Planarity :  0.004   0.046   2074
  Dihedral  : 19.485 160.201   3465
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.98 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 16.38 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.23), residues: 1333
  helix:  1.00 (0.21), residues: 637
  sheet:  0.18 (0.51), residues: 104
  loop : -0.09 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 215 
 TYR   0.018   0.002   TYR A 155 
 PHE   0.012   0.002   PHE A 446 
 TRP   0.010   0.001   TRP A1136 
 HIS   0.008   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 (14660)
  covalent geometry    : angle       0.61254 (20410)
  hydrogen bonds       : bond        0.04590 (  636)
  hydrogen bonds       : angle       4.40533 ( 1729)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 41
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 PHE cc_start: 0.9682 (t80) cc_final: 0.9467 (t80)
REVERT: A  261 ASP cc_start: 0.0652 (OUTLIER) cc_final: 0.0139 (t70)
REVERT: A  294 LYS cc_start: 0.9359 (tmtt) cc_final: 0.9080 (tmtt)
REVERT: A  495 MET cc_start: 0.9104 (ttm) cc_final: 0.8856 (ttm)
REVERT: A  664 ARG cc_start: 0.9394 (OUTLIER) cc_final: 0.8863 (tmm-80)
REVERT: A  974 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8582 (ptmt)
REVERT: A 1325 LYS cc_start: 0.9344 (ptmt) cc_final: 0.9068 (tttm)
  outliers start: 23
  outliers final: 18
  residues processed: 63
  average time/residue: 0.1481
  time to fit residues: 13.4640
Evaluate side-chains
  60 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 39
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  664 ARG
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  789 LYS
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  866 LYS
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue  975 VAL
Chi-restraints excluded: chain A residue 1006 SER
Chi-restraints excluded: chain A residue 1089 MET
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1156 LYS
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1360 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 137 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 141 optimal weight:    8.9990
   chunk 21 optimal weight:    7.9990
   chunk 70 optimal weight:    0.7980
   chunk 109 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 95 optimal weight:    0.0570
   chunk 51 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.5702

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

Flipped N/Q/H residues before XYZ refinement:
A 160 HIS
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.041765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.031044 restraints weight = 94800.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.032060 restraints weight = 44948.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.032729 restraints weight = 29289.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.033136 restraints weight = 22640.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.033354 restraints weight = 19411.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14660  Z= 0.151
  Angle     :  0.542  12.241  20410  Z= 0.285
  Chirality :  0.036   0.181   2337
  Planarity :  0.003   0.043   2074
  Dihedral  : 19.411 156.772   3465
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.54 %
    Favored  : 81.31 %
  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 aren not related in a simple way.
  whole:  0.82 (0.23), residues: 1333
  helix:  1.19 (0.21), residues: 634
  sheet:  0.21 (0.52), residues: 104
  loop :  0.02 (0.27), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 215 
 TYR   0.016   0.001   TYR A 192 
 PHE   0.009   0.001   PHE A 575 
 TRP   0.005   0.001   TRP A 883 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (14660)
  covalent geometry    : angle       0.54183 (20410)
  hydrogen bonds       : bond        0.03734 (  636)
  hydrogen bonds       : angle       4.20272 ( 1729)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 40
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 PHE cc_start: 0.9677 (t80) cc_final: 0.9457 (t80)
REVERT: A  261 ASP cc_start: 0.0722 (OUTLIER) cc_final: 0.0207 (t70)
REVERT: A  294 LYS cc_start: 0.9389 (tmtt) cc_final: 0.9115 (tmtt)
REVERT: A  495 MET cc_start: 0.9112 (ttm) cc_final: 0.8848 (ttm)
REVERT: A  664 ARG cc_start: 0.9405 (OUTLIER) cc_final: 0.8908 (tmm-80)
REVERT: A  974 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8555 (ptmt)
REVERT: A 1325 LYS cc_start: 0.9312 (ptmt) cc_final: 0.9043 (tttm)
  outliers start: 26
  outliers final: 15
  residues processed: 65
  average time/residue: 0.1514
  time to fit residues: 14.3716
Evaluate side-chains
  57 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  664 ARG
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue 1006 SER
Chi-restraints excluded: chain A residue 1014 LYS
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1156 LYS
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1360 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 142 optimal weight:    8.9990
   chunk 67 optimal weight:    4.9990
   chunk 55 optimal weight:    0.2980
   chunk 27 optimal weight:    5.9990
   chunk 20 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 63 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 135 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    2.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 160 HIS
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.041008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.030430 restraints weight = 95802.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.031425 restraints weight = 45556.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.032077 restraints weight = 29499.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.032470 restraints weight = 22747.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.032676 restraints weight = 19506.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8763
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  14660  Z= 0.206
  Angle     :  0.576  11.353  20410  Z= 0.300
  Chirality :  0.037   0.176   2337
  Planarity :  0.003   0.043   2074
  Dihedral  : 19.454 158.562   3465
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.54 %
    Favored  : 80.65 %
  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 aren not related in a simple way.
  whole:  0.76 (0.23), residues: 1333
  helix:  1.18 (0.21), residues: 631
  sheet:  0.06 (0.47), residues: 127
  loop : -0.02 (0.27), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 221 
 TYR   0.016   0.001   TYR A 155 
 PHE   0.011   0.001   PHE A1105 
 TRP   0.007   0.001   TRP A1136 
 HIS   0.007   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (14660)
  covalent geometry    : angle       0.57644 (20410)
  hydrogen bonds       : bond        0.04142 (  636)
  hydrogen bonds       : angle       4.25269 ( 1729)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 41
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 PHE cc_start: 0.9677 (t80) cc_final: 0.9471 (t80)
REVERT: A  261 ASP cc_start: 0.0694 (OUTLIER) cc_final: 0.0138 (t70)
REVERT: A  294 LYS cc_start: 0.9412 (tmtt) cc_final: 0.9157 (tmtt)
REVERT: A  495 MET cc_start: 0.9132 (ttm) cc_final: 0.8887 (ttm)
REVERT: A  664 ARG cc_start: 0.9397 (OUTLIER) cc_final: 0.8895 (tmm-80)
REVERT: A  781 MET cc_start: 0.8712 (tpp) cc_final: 0.8426 (tpp)
REVERT: A  974 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8554 (ptmt)
REVERT: A 1325 LYS cc_start: 0.9329 (ptmt) cc_final: 0.9066 (tttm)
  outliers start: 22
  outliers final: 18
  residues processed: 62
  average time/residue: 0.1500
  time to fit residues: 13.4438
Evaluate side-chains
  61 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 40
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  664 ARG
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  789 LYS
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue  975 VAL
Chi-restraints excluded: chain A residue 1006 SER
Chi-restraints excluded: chain A residue 1014 LYS
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1156 LYS
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1360 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 118 optimal weight:    5.9990
   chunk 67 optimal weight:    0.7980
   chunk 71 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 104 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 127 optimal weight:    0.8980
   chunk 76 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 160 HIS
A 341 GLN
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1264 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 = 0.2992 r_free = 0.2992 target = 0.041845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.031191 restraints weight = 95641.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.032214 restraints weight = 45643.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.032896 restraints weight = 29721.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.033227 restraints weight = 22862.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.033484 restraints weight = 19941.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14660  Z= 0.134
  Angle     :  0.537  10.362  20410  Z= 0.281
  Chirality :  0.036   0.180   2337
  Planarity :  0.003   0.041   2074
  Dihedral  : 19.392 156.122   3465
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 17.12 %
    Favored  : 80.89 %
  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 aren not related in a simple way.
  whole:  0.87 (0.24), residues: 1333
  helix:  1.30 (0.21), residues: 630
  sheet:  0.26 (0.51), residues: 106
  loop : -0.03 (0.27), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 221 
 TYR   0.015   0.001   TYR A 192 
 PHE   0.010   0.001   PHE A1105 
 TRP   0.004   0.001   TRP A 883 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (14660)
  covalent geometry    : angle       0.53744 (20410)
  hydrogen bonds       : bond        0.03670 (  636)
  hydrogen bonds       : angle       4.12534 ( 1729)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 40
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 PHE cc_start: 0.9678 (t80) cc_final: 0.9473 (t80)
REVERT: A  225 LEU cc_start: 0.9017 (mm) cc_final: 0.8560 (pt)
REVERT: A  261 ASP cc_start: 0.0424 (OUTLIER) cc_final: -0.0147 (t70)
REVERT: A  294 LYS cc_start: 0.9416 (tmtt) cc_final: 0.9164 (tmtt)
REVERT: A  495 MET cc_start: 0.9122 (ttm) cc_final: 0.8860 (ttm)
REVERT: A  664 ARG cc_start: 0.9403 (OUTLIER) cc_final: 0.8882 (tmm-80)
REVERT: A  781 MET cc_start: 0.8678 (tpp) cc_final: 0.8413 (tpp)
REVERT: A  974 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8516 (ptmt)
REVERT: A 1169 MET cc_start: 0.8937 (mmm) cc_final: 0.8565 (mmm)
REVERT: A 1325 LYS cc_start: 0.9333 (ptmt) cc_final: 0.9081 (tttm)
  outliers start: 24
  outliers final: 18
  residues processed: 61
  average time/residue: 0.1558
  time to fit residues: 13.7322
Evaluate side-chains
  61 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 40
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  664 ARG
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  789 LYS
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  866 LYS
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue 1006 SER
Chi-restraints excluded: chain A residue 1014 LYS
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1156 LYS
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1360 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 139 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 115 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 141 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0070
   chunk 63 optimal weight:    1.9990
   chunk 138 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.9202

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

Flipped N/Q/H residues before XYZ refinement:
A 990 ASN
** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1261 GLN
A1264 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.042838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.032273 restraints weight = 95626.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.033280 restraints weight = 46517.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.033936 restraints weight = 30676.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.034328 restraints weight = 23766.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 14)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.034450 restraints weight = 20428.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8743
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  14660  Z= 0.116
  Angle     :  0.525  10.002  20410  Z= 0.274
  Chirality :  0.035   0.180   2337
  Planarity :  0.003   0.041   2074
  Dihedral  : 19.304 154.623   3465
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 17.62 %
    Favored  : 80.65 %
  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 aren not related in a simple way.
  whole:  0.98 (0.24), residues: 1333
  helix:  1.40 (0.21), residues: 629
  sheet:  0.18 (0.47), residues: 129
  loop :  0.03 (0.28), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 221 
 TYR   0.015   0.001   TYR A 192 
 PHE   0.009   0.001   PHE A1105 
 TRP   0.004   0.001   TRP A1136 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (14660)
  covalent geometry    : angle       0.52526 (20410)
  hydrogen bonds       : bond        0.03514 (  636)
  hydrogen bonds       : angle       4.02931 ( 1729)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 PHE cc_start: 0.9667 (t80) cc_final: 0.9445 (t80)
REVERT: A  225 LEU cc_start: 0.9062 (mm) cc_final: 0.8629 (pt)
REVERT: A  261 ASP cc_start: 0.0483 (OUTLIER) cc_final: -0.0916 (t0)
REVERT: A  294 LYS cc_start: 0.9428 (tmtt) cc_final: 0.9171 (tmtt)
REVERT: A  664 ARG cc_start: 0.9403 (OUTLIER) cc_final: 0.8873 (tmm-80)
REVERT: A  781 MET cc_start: 0.8710 (tpp) cc_final: 0.8425 (tpp)
REVERT: A  974 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8540 (ptmt)
REVERT: A 1169 MET cc_start: 0.8858 (mmm) cc_final: 0.8469 (mmm)
REVERT: A 1325 LYS cc_start: 0.9321 (ptmt) cc_final: 0.9107 (tttm)
  outliers start: 21
  outliers final: 14
  residues processed: 63
  average time/residue: 0.1571
  time to fit residues: 14.5228
Evaluate side-chains
  55 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 38
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  664 ARG
Chi-restraints excluded: chain A residue  789 LYS
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  866 LYS
Chi-restraints excluded: chain A residue  921 LEU
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue 1089 MET
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1156 LYS
Chi-restraints excluded: chain A residue 1194 LEU
Chi-restraints excluded: chain A residue 1360 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 80 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 86 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 103 optimal weight:    6.9990
   chunk 65 optimal weight:    0.2980
   chunk 83 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.041844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.031246 restraints weight = 95724.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2669 r_free = 0.2669 target = 0.032273 restraints weight = 45082.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.032940 restraints weight = 29207.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.033351 restraints weight = 22455.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.033625 restraints weight = 19160.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8737
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14660  Z= 0.153
  Angle     :  0.551   9.918  20410  Z= 0.289
  Chirality :  0.036   0.179   2337
  Planarity :  0.003   0.041   2074
  Dihedral  : 19.316 155.828   3465
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.54 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.24), residues: 1333
  helix:  1.30 (0.21), residues: 630
  sheet:  0.21 (0.46), residues: 129
  loop : -0.02 (0.28), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 221 
 TYR   0.015   0.001   TYR A 192 
 PHE   0.010   0.001   PHE A1105 
 TRP   0.006   0.001   TRP A1136 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (14660)
  covalent geometry    : angle       0.55138 (20410)
  hydrogen bonds       : bond        0.03706 (  636)
  hydrogen bonds       : angle       4.05962 ( 1729)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2230.93 seconds
wall clock time: 39 minutes 35.57 seconds (2375.57 seconds total)