Starting phenix.real_space_refine
on Wed Aug  5 19:37:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sfi_40442/08_2026/8sfi_40442.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sfi_40442/08_2026/8sfi_40442.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sfi_40442/08_2026/8sfi_40442.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sfi_40442/08_2026/8sfi_40442.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sfi_40442/08_2026/8sfi_40442.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sfi_40442/08_2026/8sfi_40442.map"
  }
  resolution = 3.5
  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=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      69      5.49       5
     S      23      5.16       5
     C    7114      2.51       5
     N    1952      2.21       5
     O    2319      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11477
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 10030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1227, 10030
          Classifications: {'peptide': 1227}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 46, 'TRANS': 1180}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 588
          Classifications: {'RNA': 28}
          Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 6, 'rna3p': 21}
    Chain: "C"
      Number of atoms: 453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 453
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
    Chain: "D"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 406
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
  Time building chain proxies: 2.14, per 1000 atoms: 0.19
  Number of scatterers: 11477
  At special positions: 0
  Unit cell: (98.294, 100.793, 147.441, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      23     16.00
     P      69     15.00
     O    2319      8.00
     N    1952      7.00
     C    7114      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 402.8 milliseconds
  

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2342

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 10 sheets defined
      54.4% alpha, 10.4% beta
      27 base pairs and 46 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 7
    Processing helix  chain 'A' and resid 26 through 35
    Processing helix  chain 'A' and resid 35 through 67
      removed outlier: 3.692A  pdb=" N   GLU A  39 " --> pdb=" O   GLY A  35 " (cutoff:3.500A)
      Proline residue:  A  52  - end of helix
    Processing helix  chain 'A' and resid 73 through 87
      removed outlier: 3.694A  pdb=" N   SER A  77 " --> pdb=" O   TRP A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 111
      removed outlier: 3.857A  pdb=" N   TYR A 109 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   PHE A 110 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 133
      removed outlier: 4.408A  pdb=" N   PHE A 133 " --> pdb=" O   TYR A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 138
      removed outlier: 3.545A  pdb=" N   LEU A 137 " --> pdb=" O   LYS A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 147
      removed outlier: 3.745A  pdb=" N   LYS A 144 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 160
    Processing helix  chain 'A' and resid 161 through 163
      No H-bonds generated for 'chain 'A' and resid 161 through 163'
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 169 through 181
      removed outlier: 3.904A  pdb=" N   VAL A 179 " --> pdb=" O   ASN A 175 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER A 181 " --> pdb=" O   LYS A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 195
    Processing helix  chain 'A' and resid 196 through 215
      removed outlier: 3.932A  pdb=" N   LYS A 200 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 230
    Processing helix  chain 'A' and resid 236 through 241
      removed outlier: 3.685A  pdb=" N   PHE A 241 " --> pdb=" O   ILE A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 249
    Processing helix  chain 'A' and resid 251 through 264
    Processing helix  chain 'A' and resid 276 through 286
    Processing helix  chain 'A' and resid 289 through 297
      removed outlier: 3.570A  pdb=" N   SER A 297 " --> pdb=" O   HIS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 344
    Processing helix  chain 'A' and resid 344 through 356
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 370 through 379
      removed outlier: 3.840A  pdb=" N   SER A 375 " --> pdb=" O   LEU A 371 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   CYS A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 396
    Processing helix  chain 'A' and resid 402 through 415
      removed outlier: 4.161A  pdb=" N   HIS A 415 " --> pdb=" O   ARG A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 427
    Processing helix  chain 'A' and resid 430 through 450
      removed outlier: 3.688A  pdb=" N   LYS A 436 " --> pdb=" O   SER A 432 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   SER A 440 " --> pdb=" O   LYS A 436 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   SER A 444 " --> pdb=" O   SER A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 482
      removed outlier: 3.509A  pdb=" N   LYS A 464 " --> pdb=" O   LYS A 460 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   LEU A 474 " --> pdb=" O   GLN A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 507
      removed outlier: 3.899A  pdb=" N   MET A 507 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 523
    Processing helix  chain 'A' and resid 548 through 553
    Processing helix  chain 'A' and resid 600 through 605
      removed outlier: 3.506A  pdb=" N   MET A 604 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 621
      removed outlier: 3.583A  pdb=" N   GLN A 620 " --> pdb=" O   THR A 616 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   THR A 621 " --> pdb=" O   ALA A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 647
      removed outlier: 3.555A  pdb=" N   TYR A 643 " --> pdb=" O   THR A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 664
      removed outlier: 3.660A  pdb=" N   ALA A 660 " --> pdb=" O   GLN A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 685
      removed outlier: 3.855A  pdb=" N   SER A 685 " --> pdb=" O   ARG A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 704
    Processing helix  chain 'A' and resid 707 through 715
    Processing helix  chain 'A' and resid 727 through 738
      removed outlier: 3.617A  pdb=" N   ILE A 731 " --> pdb=" O   ALA A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 747 through 751
      removed outlier: 3.861A  pdb=" N   ALA A 751 " --> pdb=" O   LYS A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 769
      removed outlier: 3.580A  pdb=" N   PHE A 769 " --> pdb=" O   TRP A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 776
    Processing helix  chain 'A' and resid 861 through 865
      removed outlier: 3.584A  pdb=" N   THR A 865 " --> pdb=" O   ARG A 862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 899
    Processing helix  chain 'A' and resid 940 through 954
      removed outlier: 3.502A  pdb=" N   VAL A 952 " --> pdb=" O   GLU A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 957 through 987
      removed outlier: 3.936A  pdb=" N   GLY A 962 " --> pdb=" O   TRP A 958 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   THR A 963 " --> pdb=" O   SER A 959 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   HIS A 977 " --> pdb=" O   SER A 973 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLU A 978 " --> pdb=" O   GLN A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1008 through 1025
      removed outlier: 4.009A  pdb=" N   CYS A1025 " --> pdb=" O   ASP A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1090 through 1100
    Processing helix  chain 'A' and resid 1177 through 1189
    Processing helix  chain 'A' and resid 1200 through 1205
      removed outlier: 3.964A  pdb=" N   GLU A1205 " --> pdb=" O   PRO A1201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1208 through 1224
    Processing helix  chain 'A' and resid 1250 through 1254
    Processing helix  chain 'A' and resid 1261 through 1284
      removed outlier: 3.603A  pdb=" N   SER A1284 " --> pdb=" O   HIS A1280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1294 through 1306
    Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 533
      removed outlier: 4.492A  pdb=" N   LEU A 787 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   PHE A 869 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 4.908A  pdb=" N   TYR A 563 " --> pdb=" O   ILE A 745 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   LEU A 556 " --> pdb=" O   MET A 593 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   MET A 593 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533
      removed outlier: 4.492A  pdb=" N   LEU A 787 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 366
    Processing sheet with id=AA4, first strand: chain 'A' and resid 596 through 597
    Processing sheet with id=AA5, first strand: chain 'A' and resid 626 through 628
    Processing sheet with id=AA6, first strand: chain 'A' and resid 926 through 931
      removed outlier: 4.333A  pdb=" N   GLU A 993 " --> pdb=" O   ILE A 907 " (cutoff:3.500A)
      removed outlier: 8.515A  pdb=" N   ARG A 909 " --> pdb=" O   GLU A 993 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL A1065 " --> pdb=" O   LEU A 992 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1103 through 1107
      removed outlier: 3.980A  pdb=" N   PHE A1103 " --> pdb=" O   HIS A1116 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1145 through 1147
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1159 through 1165
      removed outlier: 6.612A  pdb=" N   ARG A1159 " --> pdb=" O   ARG A1174 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   ARG A1174 " --> pdb=" O   ARG A1159 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   VAL A1161 " --> pdb=" O   ARG A1172 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   ARG A1172 " --> pdb=" O   VAL A1161 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   VAL A1163 " --> pdb=" O   THR A1170 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1226 through 1228

    506 hydrogen bonds defined for protein.
    1419 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      64 hydrogen bonds
      124 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      46 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2956
        1.34 -     1.46: 2772
        1.46 -     1.58: 5970
        1.58 -     1.70: 138
        1.70 -     1.82: 38
  Bond restraints: 11874
  Sorted by residual:
  bond pdb=" CB  PRO A 648 "
       pdb=" CG  PRO A 648 "
    ideal  model  delta    sigma   weight residual
    1.492  1.654 -0.162 5.00e-02 4.00e+02 1.05e+01
  bond pdb=" C3'  DG D  15 "
       pdb=" C2'  DG D  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 8.00e-03 1.56e+04 7.39e+00
  bond pdb=" CB  LYS A 468 "
       pdb=" CG  LYS A 468 "
    ideal  model  delta    sigma   weight residual
    1.520  1.601 -0.081 3.00e-02 1.11e+03 7.24e+00
  bond pdb=" C3'  DT D  16 "
       pdb=" C2'  DT D  16 "
    ideal  model  delta    sigma   weight residual
    1.516  1.537 -0.021 8.00e-03 1.56e+04 6.75e+00
  bond pdb=" C1'  DT D  16 "
       pdb=" N1   DT D  16 "
    ideal  model  delta    sigma   weight residual
    1.468  1.501 -0.033 1.40e-02 5.10e+03 5.55e+00
  ... (remaining 11869 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.71: 15943
        2.71 -     5.42: 272
        5.42 -     8.13: 64
        8.13 -    10.84: 55
       10.84 -    13.55: 13
  Bond angle restraints: 16347
  Sorted by residual:
  angle pdb=" CA  PRO A 648 "
        pdb=" N   PRO A 648 "
        pdb=" CD  PRO A 648 "
      ideal   model   delta    sigma   weight residual
     112.00   98.45   13.55 1.40e+00 5.10e-01 9.37e+01
  angle pdb=" N   ASP A 939 "
        pdb=" CA  ASP A 939 "
        pdb=" C   ASP A 939 "
      ideal   model   delta    sigma   weight residual
     110.24  118.36   -8.12 1.30e+00 5.92e-01 3.90e+01
  angle pdb=" C1'   U B   4 "
        pdb=" N1    U B   4 "
        pdb=" C2    U B   4 "
      ideal   model   delta    sigma   weight residual
     117.70  124.54   -6.84 1.20e+00 6.94e-01 3.25e+01
  angle pdb=" CB  LYS A 468 "
        pdb=" CG  LYS A 468 "
        pdb=" CD  LYS A 468 "
      ideal   model   delta    sigma   weight residual
     111.30  123.87  -12.57 2.30e+00 1.89e-01 2.99e+01
  angle pdb=" C   PHE A 938 "
        pdb=" CA  PHE A 938 "
        pdb=" CB  PHE A 938 "
      ideal   model   delta    sigma   weight residual
     111.74  120.37   -8.63 1.59e+00 3.96e-01 2.95e+01
  ... (remaining 16342 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.65: 6491
       30.65 -    61.29: 550
       61.29 -    91.94: 38
       91.94 -   122.58: 0
      122.58 -   153.23: 2
  Dihedral angle restraints: 7081
    sinusoidal: 3463
      harmonic: 3618
  Sorted by residual:
  dihedral pdb=" O4'   C B  11 "
           pdb=" C1'   C B  11 "
           pdb=" N1    C B  11 "
           pdb=" C2    C B  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   46.77  153.23     1      1.50e+01 4.44e-03 8.08e+01
  dihedral pdb=" O4'   U B  12 "
           pdb=" C1'   U B  12 "
           pdb=" N1    U B  12 "
           pdb=" C2    U B  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   53.50  146.50     1      1.50e+01 4.44e-03 7.82e+01
  dihedral pdb=" CA  THR A 522 "
           pdb=" C   THR A 522 "
           pdb=" N   LYS A 523 "
           pdb=" CA  LYS A 523 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.50  -25.50     0      5.00e+00 4.00e-02 2.60e+01
  ... (remaining 7078 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 1668
       0.104 -    0.208: 127
       0.208 -    0.311: 4
       0.311 -    0.415: 11
       0.415 -    0.519: 6
  Chirality restraints: 1816
  Sorted by residual:
  chirality pdb=" CG  LEU A 471 "
            pdb=" CB  LEU A 471 "
            pdb=" CD1 LEU A 471 "
            pdb=" CD2 LEU A 471 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.07   -0.52 2.00e-01 2.50e+01 6.73e+00
  chirality pdb=" P    DC C  26 "
            pdb=" OP1  DC C  26 "
            pdb=" OP2  DC C  26 "
            pdb=" O5'  DC C  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.77   -0.44 2.00e-01 2.50e+01 4.76e+00
  chirality pdb=" P    DA D  14 "
            pdb=" OP1  DA D  14 "
            pdb=" OP2  DA D  14 "
            pdb=" O5'  DA D  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.76   -0.43 2.00e-01 2.50e+01 4.61e+00
  ... (remaining 1813 not shown)

  Planarity restraints: 1852
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 605 "    0.089 5.00e-02 4.00e+02   1.32e-01 2.78e+01
        pdb=" N   PRO A 606 "   -0.228 5.00e-02 4.00e+02
        pdb=" CA  PRO A 606 "    0.068 5.00e-02 4.00e+02
        pdb=" CD  PRO A 606 "    0.071 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 537 "   -0.068 5.00e-02 4.00e+02   1.04e-01 1.72e+01
        pdb=" N   PRO A 538 "    0.179 5.00e-02 4.00e+02
        pdb=" CA  PRO A 538 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO A 538 "   -0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 647 "   -0.065 5.00e-02 4.00e+02   9.01e-02 1.30e+01
        pdb=" N   PRO A 648 "    0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO A 648 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 648 "   -0.049 5.00e-02 4.00e+02
  ... (remaining 1849 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1305
        2.75 -     3.29: 11003
        3.29 -     3.83: 20297
        3.83 -     4.36: 23053
        4.36 -     4.90: 38033
  Nonbonded interactions: 93691
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 441 "
            pdb=" OG  SER A 444 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   ASN A1090 "
            pdb=" OG  SER A1093 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OH  TYR A  11 "
            pdb=" OD1 ASN A1024 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   GLN A 437 "
            pdb=" OG  SER A 440 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   LYS A 429 "
            pdb=" OG  SER A 432 "
     model   vdw
     2.300 3.040
  ... (remaining 93686 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:             2.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.750
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
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   0.162  11874  Z= 0.295
  Angle     :  1.109  13.549  16347  Z= 0.625
  Chirality :  0.066   0.519   1816
  Planarity :  0.008   0.132   1852
  Dihedral  : 19.823 153.226   4739
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 24.27 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.23), residues: 1219
  helix: -0.55 (0.20), residues: 589
  sheet: -0.85 (0.42), residues: 148
  loop : -0.59 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 160 
 TYR   0.030   0.002   TYR A 746 
 PHE   0.049   0.003   PHE A1117 
 TRP   0.028   0.002   TRP A1085 
 HIS   0.006   0.001   HIS A 445 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00524 /  0.30 (11874)
  covalent geometry    : angle       1.10923 /  0.63 (16347)
  hydrogen bonds       : bond        0.13099 /  8.99 (  561)
  hydrogen bonds       : angle       5.87020 /  4.17 ( 1543)

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

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

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  522 THR cc_start: 0.8148 (m) cc_final: 0.7882 (t)
  outliers start: 5
  outliers final: 2
  residues processed: 101
  average time/residue: 0.0821
  time to fit residues: 12.4745
Evaluate side-chains
  58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue 1192 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:   10.0000
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:    7.9990
   chunk 35 optimal weight:    0.0970
   overall best weight:    0.6578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1044 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 = 0.3362 r_free = 0.3362 target = 0.055784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.038814 restraints weight = 66072.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.040012 restraints weight = 30990.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.040730 restraints weight = 20201.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.041130 restraints weight = 15959.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.041347 restraints weight = 14152.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  11874  Z= 0.131
  Angle     :  0.634   9.221  16347  Z= 0.335
  Chirality :  0.042   0.254   1816
  Planarity :  0.005   0.073   1852
  Dihedral  : 18.384 151.655   2219
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 22.26 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.24), residues: 1219
  helix:  0.64 (0.21), residues: 604
  sheet: -0.90 (0.42), residues: 150
  loop : -0.48 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 160 
 TYR   0.018   0.001   TYR A 173 
 PHE   0.030   0.001   PHE A 496 
 TRP   0.012   0.001   TRP A1085 
 HIS   0.004   0.001   HIS A 445 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.13 (11874)
  covalent geometry    : angle       0.63392 /  0.33 (16347)
  hydrogen bonds       : bond        0.04053 /  2.70 (  561)
  hydrogen bonds       : angle       4.61405 /  3.23 ( 1543)

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

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

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7578 (tpt) cc_final: 0.7189 (tpt)
REVERT: A  507 MET cc_start: 0.9361 (ppp) cc_final: 0.9077 (ppp)
REVERT: A  600 ASP cc_start: 0.8423 (t0) cc_final: 0.8026 (t0)
REVERT: A  604 MET cc_start: 0.9211 (mmm) cc_final: 0.8984 (mmm)
REVERT: A  619 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.9211 (m-80)
REVERT: A  908 ASP cc_start: 0.7801 (t0) cc_final: 0.7352 (t0)
REVERT: A 1017 LYS cc_start: 0.9549 (OUTLIER) cc_final: 0.9241 (tptm)
REVERT: A 1260 MET cc_start: 0.8931 (mmt) cc_final: 0.8718 (mmm)
  outliers start: 21
  outliers final: 6
  residues processed: 82
  average time/residue: 0.0710
  time to fit residues: 9.1797
Evaluate side-chains
  63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  368 HIS
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  934 THR
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue 1017 LYS
Chi-restraints excluded: chain A residue 1192 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 127 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9990
   chunk 126 optimal weight:   20.0000
   chunk 47 optimal weight:    1.9990
   chunk 39 optimal weight:   30.0000
   chunk 83 optimal weight:   10.0000
   chunk 70 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1227 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.053375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.036492 restraints weight = 68160.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.037580 restraints weight = 32920.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.038231 restraints weight = 21968.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.038588 restraints weight = 17631.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.038794 restraints weight = 15586.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  11874  Z= 0.222
  Angle     :  0.626   7.107  16347  Z= 0.337
  Chirality :  0.042   0.197   1816
  Planarity :  0.004   0.062   1852
  Dihedral  : 18.358 150.981   2218
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.71 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.53 %
    Favored  : 76.46 %
  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 are not related in a simple way.
  whole:  0.62 (0.24), residues: 1219
  helix:  1.24 (0.22), residues: 610
  sheet: -0.96 (0.41), residues: 157
  loop : -0.07 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 947 
 TYR   0.015   0.001   TYR A  61 
 PHE   0.022   0.002   PHE A 938 
 TRP   0.012   0.002   TRP A 544 
 HIS   0.007   0.001   HIS A 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00466 /  0.22 (11874)
  covalent geometry    : angle       0.62615 /  0.34 (16347)
  hydrogen bonds       : bond        0.04173 /  2.74 (  561)
  hydrogen bonds       : angle       4.36567 /  3.08 ( 1543)

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

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

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 49
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7748 (tpt) cc_final: 0.7530 (tpt)
REVERT: A   20 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7647 (tm-30)
REVERT: A  507 MET cc_start: 0.9384 (ppp) cc_final: 0.9082 (ppp)
REVERT: A  600 ASP cc_start: 0.8789 (t0) cc_final: 0.8313 (t0)
REVERT: A  604 MET cc_start: 0.9330 (mmm) cc_final: 0.9090 (mmm)
REVERT: A  908 ASP cc_start: 0.8103 (t0) cc_final: 0.7632 (t0)
REVERT: A  992 LEU cc_start: 0.9501 (mt) cc_final: 0.9273 (mm)
REVERT: A 1013 GLN cc_start: 0.9478 (mt0) cc_final: 0.9163 (mt0)
REVERT: A 1017 LYS cc_start: 0.9559 (tptm) cc_final: 0.9296 (tptm)
REVERT: A 1260 MET cc_start: 0.9003 (mmt) cc_final: 0.8609 (mmm)
  outliers start: 33
  outliers final: 20
  residues processed: 78
  average time/residue: 0.0674
  time to fit residues: 8.2661
Evaluate side-chains
  67 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 47
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  960 VAL
Chi-restraints excluded: chain A residue  984 ILE
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1239 SER
Chi-restraints excluded: chain A residue 1270 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 35 optimal weight:    0.0050
   chunk 44 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 122 optimal weight:   20.0000
   chunk 119 optimal weight:    7.9990
   chunk 73 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0270
   chunk 51 optimal weight:    0.0050
   chunk 9 optimal weight:    6.9990
   overall best weight:    1.4070

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 ASN ** 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 = 0.3330 r_free = 0.3330 target = 0.053915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.036940 restraints weight = 67573.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.038059 restraints weight = 32769.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.038719 restraints weight = 21755.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.039106 restraints weight = 17411.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.039238 restraints weight = 15415.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  11874  Z= 0.126
  Angle     :  0.542   8.073  16347  Z= 0.292
  Chirality :  0.040   0.175   1816
  Planarity :  0.004   0.053   1852
  Dihedral  : 18.376 150.845   2218
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.13 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.98 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.25), residues: 1219
  helix:  1.58 (0.22), residues: 609
  sheet: -0.78 (0.41), residues: 154
  loop : -0.05 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1127 
 TYR   0.013   0.001   TYR A  61 
 PHE   0.012   0.001   PHE A 938 
 TRP   0.019   0.001   TRP A1085 
 HIS   0.004   0.001   HIS A 191 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.13 (11874)
  covalent geometry    : angle       0.54213 /  0.29 (16347)
  hydrogen bonds       : bond        0.03386 /  2.20 (  561)
  hydrogen bonds       : angle       4.10871 /  2.89 ( 1543)

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

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

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 49
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7805 (tpt) cc_final: 0.7516 (tpt)
REVERT: A   20 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: A  507 MET cc_start: 0.9389 (ppp) cc_final: 0.9051 (ppp)
REVERT: A  600 ASP cc_start: 0.8738 (t0) cc_final: 0.8196 (t0)
REVERT: A  604 MET cc_start: 0.9324 (mmm) cc_final: 0.9088 (mmm)
REVERT: A  651 GLU cc_start: 0.9141 (mp0) cc_final: 0.8843 (mp0)
REVERT: A  908 ASP cc_start: 0.8084 (t0) cc_final: 0.7612 (t0)
  outliers start: 27
  outliers final: 18
  residues processed: 72
  average time/residue: 0.0691
  time to fit residues: 8.0355
Evaluate side-chains
  64 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   65 CYS
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue 1017 LYS
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1192 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 113 optimal weight:   10.0000
   chunk 54 optimal weight:    8.9990
   chunk 44 optimal weight:    9.9990
   chunk 31 optimal weight:    8.9990
   chunk 12 optimal weight:    8.9990
   chunk 70 optimal weight:    7.9990
   chunk 102 optimal weight:    7.9990
   chunk 117 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 36 optimal weight:   40.0000
   overall best weight:    7.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 107 HIS
A 206 HIS
A 224 ASN
A 647 ASN
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.049788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.033073 restraints weight = 71507.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.034120 restraints weight = 34676.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.034719 restraints weight = 23292.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.035051 restraints weight = 18830.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.035224 restraints weight = 16873.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.083  11874  Z= 0.448
  Angle     :  0.830  10.312  16347  Z= 0.439
  Chirality :  0.048   0.240   1816
  Planarity :  0.005   0.060   1852
  Dihedral  : 18.618 153.269   2218
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.02 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 18.34 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.24), residues: 1219
  helix:  1.16 (0.21), residues: 616
  sheet: -1.23 (0.40), residues: 157
  loop : -0.20 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 681 
 TYR   0.023   0.003   TYR A  61 
 PHE   0.026   0.003   PHE A 201 
 TRP   0.023   0.003   TRP A 544 
 HIS   0.012   0.002   HIS A 761 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00911 /  0.45 (11874)
  covalent geometry    : angle       0.83036 /  0.44 (16347)
  hydrogen bonds       : bond        0.05891 /  3.81 (  561)
  hydrogen bonds       : angle       4.72676 /  3.36 ( 1543)

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

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

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 43
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7911 (tm-30)
REVERT: A   51 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9043 (ttmt)
REVERT: A  507 MET cc_start: 0.9442 (ppp) cc_final: 0.9175 (ppp)
REVERT: A  600 ASP cc_start: 0.9248 (t0) cc_final: 0.8866 (t0)
REVERT: A  604 MET cc_start: 0.9349 (mmm) cc_final: 0.9078 (mmm)
REVERT: A  651 GLU cc_start: 0.9151 (mp0) cc_final: 0.8900 (mp0)
REVERT: A  908 ASP cc_start: 0.8346 (t0) cc_final: 0.7839 (t0)
REVERT: A 1013 GLN cc_start: 0.9539 (mt0) cc_final: 0.9228 (mt0)
REVERT: A 1014 GLN cc_start: 0.9562 (tp40) cc_final: 0.8988 (tp40)
REVERT: A 1017 LYS cc_start: 0.9571 (OUTLIER) cc_final: 0.9299 (tptm)
REVERT: A 1018 MET cc_start: 0.9533 (mtm) cc_final: 0.9056 (mtm)
REVERT: A 1225 MET cc_start: 0.9080 (mmm) cc_final: 0.8588 (mmm)
REVERT: A 1243 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8576 (p0)
  outliers start: 48
  outliers final: 28
  residues processed: 86
  average time/residue: 0.0762
  time to fit residues: 10.2639
Evaluate side-chains
  69 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 38
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   88 THR
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  568 MET
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  760 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  982 LEU
Chi-restraints excluded: chain A residue 1017 LYS
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1058 GLN
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1199 ILE
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1243 ASP
Chi-restraints excluded: chain A residue 1290 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 122 optimal weight:   10.0000
   chunk 110 optimal weight:    0.9990
   chunk 125 optimal weight:   10.0000
   chunk 96 optimal weight:    0.9980
   chunk 124 optimal weight:   10.0000
   chunk 79 optimal weight:    0.9990
   chunk 92 optimal weight:    9.9990
   chunk 50 optimal weight:    0.0010
   chunk 31 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9980
   chunk 101 optimal weight:   10.0000
   overall best weight:    0.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 206 HIS
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 447 HIS
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 ASN ** 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 = 0.3276 r_free = 0.3276 target = 0.052279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.035253 restraints weight = 68586.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.036384 restraints weight = 32862.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.037008 restraints weight = 21804.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.037386 restraints weight = 17480.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.037595 restraints weight = 15557.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  11874  Z= 0.124
  Angle     :  0.582  11.724  16347  Z= 0.308
  Chirality :  0.042   0.306   1816
  Planarity :  0.004   0.049   1852
  Dihedral  : 18.553 152.498   2218
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.38 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 20.71 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.25), residues: 1219
  helix:  1.57 (0.21), residues: 623
  sheet: -0.89 (0.41), residues: 154
  loop :  0.06 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A1306 
 TYR   0.017   0.002   TYR A  61 
 PHE   0.021   0.001   PHE A 496 
 TRP   0.023   0.002   TRP A1085 
 HIS   0.004   0.001   HIS A1269 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.12 (11874)
  covalent geometry    : angle       0.58183 /  0.31 (16347)
  hydrogen bonds       : bond        0.03536 /  2.25 (  561)
  hydrogen bonds       : angle       4.03359 /  2.83 ( 1543)

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

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

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 43
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7769 (tm-30)
REVERT: A   51 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9029 (ttmt)
REVERT: A  159 LEU cc_start: 0.9803 (tt) cc_final: 0.9382 (pp)
REVERT: A  507 MET cc_start: 0.9439 (ppp) cc_final: 0.8985 (ppp)
REVERT: A  600 ASP cc_start: 0.9046 (t0) cc_final: 0.8618 (t0)
REVERT: A  604 MET cc_start: 0.9341 (mmm) cc_final: 0.9125 (mmm)
REVERT: A  651 GLU cc_start: 0.9143 (mp0) cc_final: 0.8899 (mp0)
REVERT: A  908 ASP cc_start: 0.8370 (t0) cc_final: 0.7936 (t0)
REVERT: A 1017 LYS cc_start: 0.9499 (OUTLIER) cc_final: 0.9182 (tptm)
  outliers start: 25
  outliers final: 16
  residues processed: 64
  average time/residue: 0.0749
  time to fit residues: 7.3888
Evaluate side-chains
  60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   88 THR
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  447 HIS
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  944 LEU
Chi-restraints excluded: chain A residue 1017 LYS
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1199 ILE
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1278 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 109 optimal weight:    0.2980
   chunk 79 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 39 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 ASN ** 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 = 0.3279 r_free = 0.3279 target = 0.052382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.035390 restraints weight = 68840.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.036480 restraints weight = 32719.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.037119 restraints weight = 21931.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.037498 restraints weight = 17530.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.037708 restraints weight = 15594.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11874  Z= 0.121
  Angle     :  0.554  11.633  16347  Z= 0.291
  Chirality :  0.040   0.188   1816
  Planarity :  0.003   0.049   1852
  Dihedral  : 18.447 152.984   2218
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.63 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 20.35 %
    Favored  : 77.46 %
  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 are not related in a simple way.
  whole:  1.19 (0.25), residues: 1219
  helix:  1.76 (0.22), residues: 615
  sheet: -0.81 (0.41), residues: 154
  loop :  0.16 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1306 
 TYR   0.015   0.001   TYR A  61 
 PHE   0.019   0.001   PHE A 435 
 TRP   0.016   0.001   TRP A1085 
 HIS   0.003   0.001   HIS A1269 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.12 (11874)
  covalent geometry    : angle       0.55389 /  0.29 (16347)
  hydrogen bonds       : bond        0.03359 /  2.15 (  561)
  hydrogen bonds       : angle       3.95950 /  2.78 ( 1543)

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

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

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 46
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7737 (tm-30)
REVERT: A   51 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9005 (ttmt)
REVERT: A  159 LEU cc_start: 0.9808 (tt) cc_final: 0.9398 (pp)
REVERT: A  307 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8346 (ptmm)
REVERT: A  507 MET cc_start: 0.9446 (ppp) cc_final: 0.8961 (ppp)
REVERT: A  600 ASP cc_start: 0.9002 (t0) cc_final: 0.8540 (t0)
REVERT: A  604 MET cc_start: 0.9376 (mmm) cc_final: 0.9166 (mmm)
REVERT: A  651 GLU cc_start: 0.9153 (mp0) cc_final: 0.8911 (mp0)
REVERT: A  908 ASP cc_start: 0.8367 (t0) cc_final: 0.7954 (t0)
  outliers start: 24
  outliers final: 18
  residues processed: 67
  average time/residue: 0.0758
  time to fit residues: 7.9301
Evaluate side-chains
  65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 45
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  944 LEU
Chi-restraints excluded: chain A residue 1017 LYS
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1199 ILE
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1278 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   chunk 69 optimal weight:    4.9990
   chunk 49 optimal weight:   20.0000
   chunk 124 optimal weight:   10.0000
   chunk 110 optimal weight:    9.9990
   chunk 122 optimal weight:   20.0000
   chunk 73 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   overall best weight:    4.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 ASN ** 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 = 0.3243 r_free = 0.3243 target = 0.050788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.033815 restraints weight = 70380.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.034868 restraints weight = 34187.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.035471 restraints weight = 23027.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.035837 restraints weight = 18707.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.036059 restraints weight = 16594.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.3622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  11874  Z= 0.272
  Angle     :  0.644  12.406  16347  Z= 0.336
  Chirality :  0.043   0.215   1816
  Planarity :  0.004   0.051   1852
  Dihedral  : 18.509 153.644   2218
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.45 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.62 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.25), residues: 1219
  helix:  1.69 (0.21), residues: 622
  sheet: -1.06 (0.41), residues: 154
  loop :  0.14 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1306 
 TYR   0.020   0.002   TYR A  61 
 PHE   0.020   0.002   PHE A 496 
 TRP   0.015   0.002   TRP A 544 
 HIS   0.006   0.001   HIS A 107 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00564 /  0.27 (11874)
  covalent geometry    : angle       0.64383 /  0.34 (16347)
  hydrogen bonds       : bond        0.04158 /  2.66 (  561)
  hydrogen bonds       : angle       4.13872 /  2.92 ( 1543)

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

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

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 44
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7878 (tm-30)
REVERT: A  159 LEU cc_start: 0.9824 (tt) cc_final: 0.9432 (pp)
REVERT: A  307 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8501 (ptmm)
REVERT: A  353 PHE cc_start: 0.9113 (m-10) cc_final: 0.8866 (m-80)
REVERT: A  507 MET cc_start: 0.9454 (ppp) cc_final: 0.8950 (ppp)
REVERT: A  544 TRP cc_start: 0.9403 (OUTLIER) cc_final: 0.8559 (m100)
REVERT: A  600 ASP cc_start: 0.9154 (t0) cc_final: 0.8769 (t0)
REVERT: A  604 MET cc_start: 0.9360 (mmm) cc_final: 0.9154 (mmm)
REVERT: A  651 GLU cc_start: 0.9169 (mp0) cc_final: 0.8936 (mp0)
REVERT: A  908 ASP cc_start: 0.8475 (t0) cc_final: 0.7970 (t0)
REVERT: A 1013 GLN cc_start: 0.9526 (mt0) cc_final: 0.9107 (mt0)
REVERT: A 1018 MET cc_start: 0.9511 (mtm) cc_final: 0.9193 (mtm)
REVERT: A 1243 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8529 (p0)
  outliers start: 28
  outliers final: 21
  residues processed: 70
  average time/residue: 0.0785
  time to fit residues: 8.5023
Evaluate side-chains
  68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 44
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   88 THR
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  544 TRP
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  944 LEU
Chi-restraints excluded: chain A residue 1017 LYS
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1199 ILE
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1243 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 74 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 49 optimal weight:   20.0000
   chunk 114 optimal weight:    1.9990
   chunk 67 optimal weight:    0.4980
   chunk 112 optimal weight:    5.9990
   chunk 66 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    1.2184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  70 GLN
A 308 GLN
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 ASN ** 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 = 0.3270 r_free = 0.3270 target = 0.051909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.034997 restraints weight = 68487.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.036108 restraints weight = 32904.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.036722 restraints weight = 21884.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.037092 restraints weight = 17545.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.037293 restraints weight = 15632.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.3578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11874  Z= 0.120
  Angle     :  0.559  13.598  16347  Z= 0.290
  Chirality :  0.040   0.195   1816
  Planarity :  0.003   0.048   1852
  Dihedral  : 18.467 153.375   2218
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.71 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 20.44 %
    Favored  : 77.65 %
  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 are not related in a simple way.
  whole:  1.30 (0.25), residues: 1219
  helix:  1.84 (0.22), residues: 621
  sheet: -0.87 (0.41), residues: 154
  loop :  0.25 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 499 
 TYR   0.016   0.001   TYR A  61 
 PHE   0.019   0.001   PHE A 435 
 TRP   0.020   0.002   TRP A1085 
 HIS   0.004   0.001   HIS A1269 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.12 (11874)
  covalent geometry    : angle       0.55913 /  0.29 (16347)
  hydrogen bonds       : bond        0.03318 /  2.13 (  561)
  hydrogen bonds       : angle       3.91842 /  2.75 ( 1543)

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

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

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 46
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7801 (tm-30)
REVERT: A  159 LEU cc_start: 0.9809 (tt) cc_final: 0.9421 (pp)
REVERT: A  307 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8353 (ptmm)
REVERT: A  353 PHE cc_start: 0.9125 (m-10) cc_final: 0.8879 (m-80)
REVERT: A  507 MET cc_start: 0.9456 (ppp) cc_final: 0.8938 (ppp)
REVERT: A  600 ASP cc_start: 0.9066 (t0) cc_final: 0.8629 (t0)
REVERT: A  651 GLU cc_start: 0.9163 (mp0) cc_final: 0.8936 (mp0)
REVERT: A  908 ASP cc_start: 0.8431 (t0) cc_final: 0.7974 (t0)
REVERT: A 1018 MET cc_start: 0.9505 (mtm) cc_final: 0.9190 (mtm)
  outliers start: 21
  outliers final: 19
  residues processed: 64
  average time/residue: 0.0808
  time to fit residues: 8.0541
Evaluate side-chains
  64 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 44
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   88 THR
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  944 LEU
Chi-restraints excluded: chain A residue 1017 LYS
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1199 ILE
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1302 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 125 optimal weight:   20.0000
   chunk 119 optimal weight:    8.9990
   chunk 96 optimal weight:    0.6980
   chunk 57 optimal weight:    6.9990
   chunk 19 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 124 optimal weight:   10.0000
   chunk 104 optimal weight:    6.9990
   chunk 122 optimal weight:   20.0000
   chunk 65 optimal weight:    8.9990
   overall best weight:    4.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 ASN ** 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 = 0.3241 r_free = 0.3241 target = 0.050673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.033799 restraints weight = 70798.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.034856 restraints weight = 34050.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.035472 restraints weight = 22838.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.035808 restraints weight = 18442.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.036007 restraints weight = 16296.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.3847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  11874  Z= 0.251
  Angle     :  0.631  13.227  16347  Z= 0.328
  Chirality :  0.042   0.212   1816
  Planarity :  0.004   0.047   1852
  Dihedral  : 18.501 154.120   2218
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.61 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 20.62 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.25), residues: 1219
  helix:  1.77 (0.21), residues: 624
  sheet: -1.07 (0.41), residues: 154
  loop :  0.15 (0.32), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1306 
 TYR   0.021   0.002   TYR A  61 
 PHE   0.018   0.002   PHE A 496 
 TRP   0.016   0.002   TRP A1085 
 HIS   0.005   0.001   HIS A1269 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00522 /  0.25 (11874)
  covalent geometry    : angle       0.63126 /  0.33 (16347)
  hydrogen bonds       : bond        0.04001 /  2.56 (  561)
  hydrogen bonds       : angle       4.06947 /  2.87 ( 1543)

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

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

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2438 Ramachandran restraints generated.
    1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 44
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7876 (tm-30)
REVERT: A  159 LEU cc_start: 0.9828 (tt) cc_final: 0.9432 (pp)
REVERT: A  507 MET cc_start: 0.9449 (ppp) cc_final: 0.8929 (ppp)
REVERT: A  544 TRP cc_start: 0.9393 (OUTLIER) cc_final: 0.8576 (m100)
REVERT: A  600 ASP cc_start: 0.9160 (t0) cc_final: 0.8781 (t0)
REVERT: A  604 MET cc_start: 0.9434 (mmm) cc_final: 0.8863 (mmm)
REVERT: A  651 GLU cc_start: 0.9180 (mp0) cc_final: 0.8948 (mp0)
REVERT: A  908 ASP cc_start: 0.8480 (t0) cc_final: 0.7955 (t0)
REVERT: A 1013 GLN cc_start: 0.9520 (mt0) cc_final: 0.9092 (mt0)
REVERT: A 1018 MET cc_start: 0.9502 (mtm) cc_final: 0.9194 (mtm)
  outliers start: 22
  outliers final: 20
  residues processed: 63
  average time/residue: 0.0777
  time to fit residues: 7.8243
Evaluate side-chains
  64 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   88 THR
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  526 TYR
Chi-restraints excluded: chain A residue  544 TRP
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  944 LEU
Chi-restraints excluded: chain A residue 1017 LYS
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1192 VAL
Chi-restraints excluded: chain A residue 1199 ILE
Chi-restraints excluded: chain A residue 1210 HIS
Chi-restraints excluded: chain A residue 1302 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 38 optimal weight:   40.0000
   chunk 67 optimal weight:   10.0000
   chunk 116 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 41 optimal weight:    9.9990
   chunk 108 optimal weight:    0.9980
   chunk 127 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   chunk 102 optimal weight:    9.9990
   overall best weight:    2.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 ASN ** 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 = 0.3260 r_free = 0.3260 target = 0.051472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.034468 restraints weight = 69777.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.035547 restraints weight = 33439.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.036162 restraints weight = 22378.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.036518 restraints weight = 17995.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.036708 restraints weight = 16079.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11874  Z= 0.150
  Angle     :  0.571  13.997  16347  Z= 0.297
  Chirality :  0.041   0.198   1816
  Planarity :  0.003   0.045   1852
  Dihedral  : 18.478 153.863   2218
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.71 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 20.44 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.26), residues: 1219
  helix:  1.86 (0.22), residues: 624
  sheet: -0.93 (0.41), residues: 154
  loop :  0.23 (0.32), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1306 
 TYR   0.016   0.001   TYR A  61 
 PHE   0.037   0.001   PHE A 353 
 TRP   0.020   0.002   TRP A1085 
 HIS   0.004   0.001   HIS A1269 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.15 (11874)
  covalent geometry    : angle       0.57119 /  0.30 (16347)
  hydrogen bonds       : bond        0.03348 /  2.14 (  561)
  hydrogen bonds       : angle       3.91633 /  2.74 ( 1543)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1638.48 seconds
wall clock time: 29 minutes 3.98 seconds (1743.98 seconds total)