Starting phenix.real_space_refine
on Tue Mar  3 21:01:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qfw_13950/03_2026/7qfw_13950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qfw_13950/03_2026/7qfw_13950.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qfw_13950/03_2026/7qfw_13950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qfw_13950/03_2026/7qfw_13950.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qfw_13950/03_2026/7qfw_13950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qfw_13950/03_2026/7qfw_13950.map"
  }
  resolution = 3.86
  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=   0.001 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      64      5.49       5
     S      32      5.16       5
     C    5395      2.51       5
     N    1492      2.21       5
     O    1782      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8765
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 823, 6643
          Classifications: {'peptide': 823}
          Link IDs: {'PTRANS': 20, 'TRANS': 802}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 810
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 3, 'TRANS': 90}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 672
          Classifications: {'DNA': 32}
          Link IDs: {'rna3p': 31}
    Chain: "D"
      Number of atoms: 640
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 640
          Classifications: {'DNA': 32}
          Link IDs: {'rna3p': 31}
  Time building chain proxies: 1.84, per 1000 atoms: 0.21
  Number of scatterers: 8765
  At special positions: 0
  Unit cell: (79.04, 111.28, 132.08, 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      32     16.00
     P      64     15.00
     O    1782      8.00
     N    1492      7.00
     C    5395      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: 0.53
  Conformation dependent library (CDL) restraints added in 212.3 milliseconds
  

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1786

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 0 sheets defined
      73.9% alpha, 0.0% beta
      30 base pairs and 57 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 24
      removed outlier: 4.032A  pdb=" N   PHE A  14 " --> pdb=" O   ASN A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 49
      removed outlier: 3.811A  pdb=" N   ALA A  36 " --> pdb=" O   ARG A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 64
    Processing helix  chain 'A' and resid 72 through 98
      removed outlier: 3.737A  pdb=" N   ASP A  76 " --> pdb=" O   GLU A  72 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ILE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   LEU A  81 " --> pdb=" O   ARG A  77 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LYS A  98 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 123
      removed outlier: 3.629A  pdb=" N   ARG A 120 " --> pdb=" O   ASP A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 143
      removed outlier: 3.780A  pdb=" N   ARG A 134 " --> pdb=" O   ASP A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 149
      removed outlier: 4.112A  pdb=" N   GLY A 149 " --> pdb=" O   MET A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 167
    Processing helix  chain 'A' and resid 171 through 184
      removed outlier: 3.658A  pdb=" N   ARG A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLN A 177 " --> pdb=" O   THR A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 217
      removed outlier: 3.949A  pdb=" N   THR A 209 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 228
      removed outlier: 3.540A  pdb=" N   ALA A 225 " --> pdb=" O   GLU A 221 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LEU A 228 " --> pdb=" O   ARG A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 242
    Processing helix  chain 'A' and resid 243 through 246
    Processing helix  chain 'A' and resid 248 through 258
      removed outlier: 3.571A  pdb=" N   ARG A 252 " --> pdb=" O   ASN A 248 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   TYR A 256 " --> pdb=" O   ARG A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 264
    Processing helix  chain 'A' and resid 265 through 268
      removed outlier: 3.699A  pdb=" N   PHE A 268 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 265 through 268'
    Processing helix  chain 'A' and resid 272 through 285
      removed outlier: 3.734A  pdb=" N   GLN A 278 " --> pdb=" O   HIS A 274 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   ILE A 280 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   GLU A 281 " --> pdb=" O   ASP A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 301
      removed outlier: 3.508A  pdb=" N   ARG A 292 " --> pdb=" O   GLU A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 316
    Processing helix  chain 'A' and resid 325 through 330
    Processing helix  chain 'A' and resid 330 through 335
    Processing helix  chain 'A' and resid 338 through 344
    Processing helix  chain 'A' and resid 347 through 351
      removed outlier: 3.791A  pdb=" N   ILE A 350 " --> pdb=" O   PRO A 347 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   TRP A 351 " --> pdb=" O   GLU A 348 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 347 through 351'
    Processing helix  chain 'A' and resid 355 through 372
    Processing helix  chain 'A' and resid 374 through 380
    Processing helix  chain 'A' and resid 384 through 401
    Processing helix  chain 'A' and resid 414 through 430
    Processing helix  chain 'A' and resid 436 through 451
    Processing helix  chain 'A' and resid 457 through 471
    Processing helix  chain 'A' and resid 474 through 500
      removed outlier: 3.681A  pdb=" N   PHE A 478 " --> pdb=" O   ASN A 474 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASP A 493 " --> pdb=" O   ILE A 489 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS A 496 " --> pdb=" O   ASP A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 587
      removed outlier: 3.502A  pdb=" N   ILE A 575 " --> pdb=" O   SER A 571 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ARG A 581 " --> pdb=" O   LEU A 577 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TYR A 584 " --> pdb=" O   THR A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 606
    Processing helix  chain 'A' and resid 607 through 612
      removed outlier: 3.655A  pdb=" N   ARG A 612 " --> pdb=" O   THR A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 631
    Processing helix  chain 'A' and resid 633 through 650
      removed outlier: 3.837A  pdb=" N   ALA A 637 " --> pdb=" O   ASP A 633 " (cutoff:3.500A)
      removed outlier: 5.482A  pdb=" N   TYR A 642 " --> pdb=" O   ILE A 638 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   ILE A 643 " --> pdb=" O   ASP A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 671
    Processing helix  chain 'A' and resid 682 through 695
    Processing helix  chain 'A' and resid 699 through 716
    Processing helix  chain 'A' and resid 722 through 734
    Processing helix  chain 'A' and resid 740 through 751
      removed outlier: 3.659A  pdb=" N   ILE A 751 " --> pdb=" O   PHE A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 758
      removed outlier: 3.760A  pdb=" N   SER A 757 " --> pdb=" O   VAL A 753 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   HIS A 758 " --> pdb=" O   TYR A 754 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 785
      removed outlier: 4.404A  pdb=" N   ALA A 770 " --> pdb=" O   SER A 766 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   ASP A 771 " --> pdb=" O   ARG A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 810
    Processing helix  chain 'A' and resid 820 through 825
      removed outlier: 3.711A  pdb=" N   LYS A 823 " --> pdb=" O   GLY A 820 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASP A 825 " --> pdb=" O   THR A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 839
    Processing helix  chain 'A' and resid 840 through 842
      No H-bonds generated for 'chain 'A' and resid 840 through 842'
    Processing helix  chain 'A' and resid 846 through 853
    Processing helix  chain 'A' and resid 854 through 858
      removed outlier: 3.886A  pdb=" N   ALA A 857 " --> pdb=" O   ASN A 854 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE A 858 " --> pdb=" O   ILE A 855 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 854 through 858'
    Processing helix  chain 'A' and resid 866 through 883
      removed outlier: 4.207A  pdb=" N   LEU A 872 " --> pdb=" O   THR A 868 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ASP A 883 " --> pdb=" O   ILE A 879 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 886 through 908
      removed outlier: 4.311A  pdb=" N   ALA A 892 " --> pdb=" O   VAL A 888 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 398
    Processing helix  chain 'B' and resid 399 through 401
      No H-bonds generated for 'chain 'B' and resid 399 through 401'
    Processing helix  chain 'B' and resid 470 through 474
    Processing helix  chain 'B' and resid 486 through 490
      removed outlier: 3.519A  pdb=" N   ASN B 489 " --> pdb=" O   PRO B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 505 through 511

    421 hydrogen bonds defined for protein.
    1248 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      60 hydrogen bonds
      120 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      57 stacking parallelities
  Total time for adding SS restraints: 1.81

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2296
        1.34 -     1.45: 1885
        1.45 -     1.57: 4689
        1.57 -     1.69: 126
        1.69 -     1.81: 50
  Bond restraints: 9046
  Sorted by residual:
  bond pdb=" CA  ASN A 672 "
       pdb=" C   ASN A 672 "
    ideal  model  delta    sigma   weight residual
    1.524  1.480  0.044 1.40e-02 5.10e+03 9.69e+00
  bond pdb=" N   GLN A  99 "
       pdb=" CA  GLN A  99 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.29e-02 6.01e+03 4.60e+00
  bond pdb=" N   ASP A 319 "
       pdb=" CA  ASP A 319 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.026 1.29e-02 6.01e+03 3.91e+00
  bond pdb=" C   ILE A 751 "
       pdb=" N   PRO A 752 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.022 1.28e-02 6.10e+03 2.92e+00
  bond pdb=" CA  GLY A 149 "
       pdb=" C   GLY A 149 "
    ideal  model  delta    sigma   weight residual
    1.530  1.513  0.018 1.04e-02 9.25e+03 2.87e+00
  ... (remaining 9041 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.09: 12299
        3.09 -     6.19: 181
        6.19 -     9.28: 10
        9.28 -    12.37: 3
       12.37 -    15.47: 1
  Bond angle restraints: 12494
  Sorted by residual:
  angle pdb=" C   LYS A  98 "
        pdb=" N   GLN A  99 "
        pdb=" CA  GLN A  99 "
      ideal   model   delta    sigma   weight residual
     121.54  130.88   -9.34 1.91e+00 2.74e-01 2.39e+01
  angle pdb=" C3'  DT D   9 "
        pdb=" O3'  DT D   9 "
        pdb=" P    DT D  10 "
      ideal   model   delta    sigma   weight residual
     120.20  127.45   -7.25 1.50e+00 4.44e-01 2.34e+01
  angle pdb=" CA  LEU A 307 "
        pdb=" CB  LEU A 307 "
        pdb=" CG  LEU A 307 "
      ideal   model   delta    sigma   weight residual
     116.30  131.77  -15.47 3.50e+00 8.16e-02 1.95e+01
  angle pdb=" C   LEU A 318 "
        pdb=" N   ASP A 319 "
        pdb=" CA  ASP A 319 "
      ideal   model   delta    sigma   weight residual
     121.54  129.70   -8.16 1.91e+00 2.74e-01 1.82e+01
  angle pdb=" CA  ARG B 411 "
        pdb=" CB  ARG B 411 "
        pdb=" CG  ARG B 411 "
      ideal   model   delta    sigma   weight residual
     114.10  121.76   -7.66 2.00e+00 2.50e-01 1.47e+01
  ... (remaining 12489 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.37: 4651
       27.37 -    54.74: 670
       54.74 -    82.11: 81
       82.11 -   109.48: 6
      109.48 -   136.84: 2
  Dihedral angle restraints: 5410
    sinusoidal: 2689
      harmonic: 2721
  Sorted by residual:
  dihedral pdb=" CA  LYS A  98 "
           pdb=" C   LYS A  98 "
           pdb=" N   GLN A  99 "
           pdb=" CA  GLN A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.13  -25.87     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  ASP B 462 "
           pdb=" C   ASP B 462 "
           pdb=" N   PHE B 463 "
           pdb=" CA  PHE B 463 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.39  -25.61     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  GLN A 818 "
           pdb=" C   GLN A 818 "
           pdb=" N   THR A 819 "
           pdb=" CA  THR A 819 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.27  -23.73     0      5.00e+00 4.00e-02 2.25e+01
  ... (remaining 5407 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 953
       0.044 -    0.088: 354
       0.088 -    0.132: 95
       0.132 -    0.175: 28
       0.175 -    0.219: 8
  Chirality restraints: 1438
  Sorted by residual:
  chirality pdb=" P    DT D  10 "
            pdb=" OP1  DT D  10 "
            pdb=" OP2  DT D  10 "
            pdb=" O5'  DT D  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.56   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  ASP A 319 "
            pdb=" N   ASP A 319 "
            pdb=" C   ASP A 319 "
            pdb=" CB  ASP A 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.89e-01
  chirality pdb=" C1'  DA C  16 "
            pdb=" O4'  DA C  16 "
            pdb=" C2'  DA C  16 "
            pdb=" N9   DA C  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.23    0.19 2.00e-01 2.50e+01 9.39e-01
  ... (remaining 1435 not shown)

  Planarity restraints: 1373
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  66 "   -0.053 5.00e-02 4.00e+02   7.94e-02 1.01e+01
        pdb=" N   PRO A  67 "    0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO A  67 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A  67 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 608 "   -0.047 5.00e-02 4.00e+02   7.09e-02 8.05e+00
        pdb=" N   PRO A 609 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 609 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 609 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 798 "    0.045 5.00e-02 4.00e+02   6.80e-02 7.41e+00
        pdb=" N   PRO A 799 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A 799 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 799 "    0.038 5.00e-02 4.00e+02
  ... (remaining 1370 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2303
        2.80 -     3.33: 8063
        3.33 -     3.85: 15330
        3.85 -     4.38: 17579
        4.38 -     4.90: 27470
  Nonbonded interactions: 70745
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 383 "
            pdb=" OH  TYR A 432 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   THR A 826 "
            pdb=" OG1 THR A 830 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   SER A 862 "
            pdb=" OG  SER A 862 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   GLU A 430 "
            pdb=" OG  SER A 470 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" O   THR A 727 "
            pdb=" OG  SER A 731 "
     model   vdw
     2.346 3.040
  ... (remaining 70740 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.700
  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:1.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6440
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      :  0.006   0.065   9046  Z= 0.287
  Angle     :  0.984  15.467  12494  Z= 0.579
  Chirality :  0.052   0.219   1438
  Planarity :  0.008   0.079   1373
  Dihedral  : 22.546 136.844   3624
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  6.92 %
    Favored  : 92.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.68 (0.20), residues: 905
  helix: -2.90 (0.14), residues: 630
  sheet:  None (None), residues: 0
  loop : -3.13 (0.29), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 322 
 TYR   0.018   0.002   TYR B 496 
 PHE   0.023   0.002   PHE A 354 
 TRP   0.014   0.002   TRP A 780 
 HIS   0.008   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 ( 9046)
  covalent geometry    : angle       0.98408 (12494)
  hydrogen bonds       : bond        0.12665 (  481)
  hydrogen bonds       : angle       6.10970 ( 1368)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 194
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.7665 (mttm) cc_final: 0.7383 (mmtp)
REVERT: A   13 ILE cc_start: 0.7989 (mm) cc_final: 0.7588 (mt)
REVERT: A   39 LYS cc_start: 0.7811 (tptt) cc_final: 0.7555 (tptt)
REVERT: A   47 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6286 (tm-30)
REVERT: A   72 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7152 (tm-30)
REVERT: A  107 GLU cc_start: 0.8005 (mp0) cc_final: 0.7696 (mm-30)
REVERT: A  136 ARG cc_start: 0.7191 (mmt-90) cc_final: 0.6952 (mmt-90)
REVERT: A  266 LYS cc_start: 0.7948 (mmmm) cc_final: 0.7733 (mtmm)
REVERT: A  285 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6819 (mm-30)
REVERT: A  384 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6239 (tm-30)
REVERT: A  421 ILE cc_start: 0.6590 (mt) cc_final: 0.6382 (mm)
REVERT: A  471 LEU cc_start: 0.7946 (tp) cc_final: 0.7728 (tp)
REVERT: A  641 MET cc_start: 0.7488 (tpp) cc_final: 0.7090 (tpt)
REVERT: A  644 LEU cc_start: 0.8161 (mt) cc_final: 0.7892 (mp)
REVERT: A  648 VAL cc_start: 0.7331 (p) cc_final: 0.7100 (p)
REVERT: A  695 LYS cc_start: 0.7067 (mttt) cc_final: 0.6844 (mttp)
REVERT: A  705 ILE cc_start: 0.8051 (pt) cc_final: 0.7700 (mt)
REVERT: A  808 PHE cc_start: 0.7944 (t80) cc_final: 0.7720 (t80)
REVERT: A  837 LYS cc_start: 0.7459 (mttm) cc_final: 0.7234 (ttmm)
REVERT: A  841 GLN cc_start: 0.7527 (mt0) cc_final: 0.7210 (tt0)
REVERT: A  895 LYS cc_start: 0.7385 (tttt) cc_final: 0.7183 (ttpt)
REVERT: B  408 TRP cc_start: 0.6047 (p-90) cc_final: 0.4805 (p-90)
  outliers start: 3
  outliers final: 0
  residues processed: 195
  average time/residue: 0.1173
  time to fit residues: 30.0216
Evaluate side-chains
  174 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN
A  31 HIS
A  34 HIS
A  42 GLN
A  71 ASN
A 121 HIS
A 216 ASN
A 372 ASN
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 401 HIS
A 402 HIS
A 613 ASN
A 697 ASN
A 758 HIS
A 884 ASN
B 401 ASN
B 495 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.162530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.139617 restraints weight = 12699.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.143307 restraints weight = 6825.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.145821 restraints weight = 4265.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.147529 restraints weight = 2998.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.148716 restraints weight = 2307.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6394
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9046  Z= 0.192
  Angle     :  0.652   8.378  12494  Z= 0.366
  Chirality :  0.041   0.180   1438
  Planarity :  0.006   0.058   1373
  Dihedral  : 24.753 138.277   1749
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 13.48 %
    Favored  : 84.84 %
  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: -2.66 (0.24), residues: 905
  helix: -1.16 (0.19), residues: 623
  sheet:  None (None), residues: 0
  loop : -2.91 (0.29), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 910 
 TYR   0.018   0.002   TYR A 657 
 PHE   0.015   0.002   PHE A 362 
 TRP   0.009   0.001   TRP A 780 
 HIS   0.007   0.001   HIS A 687 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 9046)
  covalent geometry    : angle       0.65210 (12494)
  hydrogen bonds       : bond        0.05226 (  481)
  hydrogen bonds       : angle       4.42738 ( 1368)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 181
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.7677 (mttm) cc_final: 0.7330 (mmtp)
REVERT: A   13 ILE cc_start: 0.8042 (mm) cc_final: 0.7657 (mt)
REVERT: A   19 GLU cc_start: 0.7153 (tt0) cc_final: 0.6910 (tt0)
REVERT: A   31 HIS cc_start: 0.6917 (OUTLIER) cc_final: 0.6679 (m-70)
REVERT: A   39 LYS cc_start: 0.7848 (tptt) cc_final: 0.7527 (tptt)
REVERT: A  107 GLU cc_start: 0.8020 (mp0) cc_final: 0.7711 (mm-30)
REVERT: A  118 PHE cc_start: 0.7545 (t80) cc_final: 0.7335 (t80)
REVERT: A  227 MET cc_start: 0.7436 (ttm) cc_final: 0.7213 (ttm)
REVERT: A  246 ASP cc_start: 0.7761 (t70) cc_final: 0.7548 (t70)
REVERT: A  284 LEU cc_start: 0.8382 (mt) cc_final: 0.8181 (mt)
REVERT: A  333 LEU cc_start: 0.8113 (mt) cc_final: 0.7759 (tp)
REVERT: A  421 ILE cc_start: 0.6482 (mt) cc_final: 0.6270 (mm)
REVERT: A  692 LYS cc_start: 0.7881 (mmmt) cc_final: 0.7578 (mmmt)
REVERT: A  695 LYS cc_start: 0.7122 (mttt) cc_final: 0.6909 (mttp)
REVERT: A  753 VAL cc_start: 0.8081 (p) cc_final: 0.7803 (t)
REVERT: A  841 GLN cc_start: 0.7594 (mt0) cc_final: 0.7348 (tt0)
REVERT: A  895 LYS cc_start: 0.7425 (tttt) cc_final: 0.7148 (ttpt)
REVERT: B  492 ASN cc_start: 0.8201 (t0) cc_final: 0.7758 (m-40)
  outliers start: 14
  outliers final: 4
  residues processed: 189
  average time/residue: 0.1104
  time to fit residues: 27.7928
Evaluate side-chains
  170 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 165
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 HIS
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain B residue  485 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 13 optimal weight:    0.0980
   chunk 5 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0770
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 216 ASN
** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 401 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 495 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.164096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.141212 restraints weight = 12547.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.144872 restraints weight = 6814.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.147422 restraints weight = 4280.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.149113 restraints weight = 3001.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.150346 restraints weight = 2301.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6375
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9046  Z= 0.153
  Angle     :  0.611   6.993  12494  Z= 0.342
  Chirality :  0.039   0.191   1438
  Planarity :  0.005   0.056   1373
  Dihedral  : 24.519 139.083   1749
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.11 %
    Favored  : 81.50 %
  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: -1.78 (0.26), residues: 905
  helix: -0.45 (0.20), residues: 629
  sheet:  None (None), residues: 0
  loop : -2.76 (0.31), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 581 
 TYR   0.013   0.001   TYR A 657 
 PHE   0.024   0.001   PHE A 808 
 TRP   0.010   0.001   TRP A 780 
 HIS   0.012   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9046)
  covalent geometry    : angle       0.61134 (12494)
  hydrogen bonds       : bond        0.04773 (  481)
  hydrogen bonds       : angle       4.08366 ( 1368)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 168
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.7623 (mttm) cc_final: 0.7377 (mmtp)
REVERT: A   13 ILE cc_start: 0.8077 (mm) cc_final: 0.7729 (mt)
REVERT: A   19 GLU cc_start: 0.7060 (tt0) cc_final: 0.6829 (tt0)
REVERT: A   39 LYS cc_start: 0.7847 (tptt) cc_final: 0.7547 (tptt)
REVERT: A   72 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7158 (tm-30)
REVERT: A  107 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7725 (mm-30)
REVERT: A  136 ARG cc_start: 0.7422 (tpt170) cc_final: 0.7184 (mmt-90)
REVERT: A  291 VAL cc_start: 0.7413 (m) cc_final: 0.7017 (p)
REVERT: A  333 LEU cc_start: 0.8060 (mt) cc_final: 0.7747 (tp)
REVERT: A  348 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7071 (tp30)
REVERT: A  443 MET cc_start: 0.7710 (tpp) cc_final: 0.7252 (tpt)
REVERT: A  641 MET cc_start: 0.7184 (tpt) cc_final: 0.6857 (tpt)
REVERT: A  692 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7624 (mmmt)
REVERT: A  808 PHE cc_start: 0.7949 (t80) cc_final: 0.7688 (t80)
REVERT: A  841 GLN cc_start: 0.7544 (mt0) cc_final: 0.7342 (tt0)
REVERT: B  408 TRP cc_start: 0.5658 (p-90) cc_final: 0.4595 (p-90)
REVERT: B  492 ASN cc_start: 0.8145 (t0) cc_final: 0.7722 (m-40)
  outliers start: 20
  outliers final: 10
  residues processed: 179
  average time/residue: 0.1057
  time to fit residues: 25.2730
Evaluate side-chains
  172 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 160
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   31 HIS
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  348 GLU
Chi-restraints excluded: chain A residue  644 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  888 VAL
Chi-restraints excluded: chain B residue  485 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 93 optimal weight:    4.9990
   chunk 17 optimal weight:    0.2980
   chunk 42 optimal weight:    0.2980
   chunk 38 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 72 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 401 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 670 HIS
B 495 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.164534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.141539 restraints weight = 12843.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.145329 restraints weight = 6883.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.147937 restraints weight = 4271.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.149693 restraints weight = 2961.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.150847 restraints weight = 2274.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6372
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9046  Z= 0.155
  Angle     :  0.608   6.786  12494  Z= 0.339
  Chirality :  0.040   0.191   1438
  Planarity :  0.004   0.049   1373
  Dihedral  : 24.384 141.388   1749
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.90 %
    Favored  : 79.83 %
  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: -1.33 (0.27), residues: 905
  helix: -0.11 (0.20), residues: 631
  sheet:  None (None), residues: 0
  loop : -2.61 (0.31), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 910 
 TYR   0.015   0.001   TYR A 657 
 PHE   0.022   0.001   PHE A 118 
 TRP   0.009   0.001   TRP B 408 
 HIS   0.017   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 9046)
  covalent geometry    : angle       0.60757 (12494)
  hydrogen bonds       : bond        0.04656 (  481)
  hydrogen bonds       : angle       3.93889 ( 1368)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ILE cc_start: 0.8096 (mm) cc_final: 0.7744 (mt)
REVERT: A   19 GLU cc_start: 0.7070 (tt0) cc_final: 0.6835 (tt0)
REVERT: A   39 LYS cc_start: 0.7859 (tptt) cc_final: 0.7607 (tptt)
REVERT: A   72 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7350 (tm-30)
REVERT: A  333 LEU cc_start: 0.8047 (mt) cc_final: 0.7713 (tp)
REVERT: A  431 ARG cc_start: 0.5209 (mtp180) cc_final: 0.4542 (mtp180)
REVERT: A  443 MET cc_start: 0.7717 (tpp) cc_final: 0.7262 (tpt)
REVERT: A  471 LEU cc_start: 0.8034 (tp) cc_final: 0.7813 (tp)
REVERT: A  692 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7669 (mmmt)
REVERT: A  808 PHE cc_start: 0.7968 (t80) cc_final: 0.7713 (t80)
REVERT: B  391 MET cc_start: 0.6534 (mmp) cc_final: 0.5956 (mmt)
REVERT: B  408 TRP cc_start: 0.5644 (p-90) cc_final: 0.4545 (p-90)
REVERT: B  492 ASN cc_start: 0.8043 (t0) cc_final: 0.7603 (m-40)
  outliers start: 19
  outliers final: 10
  residues processed: 171
  average time/residue: 0.1075
  time to fit residues: 24.3495
Evaluate side-chains
  164 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 154
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  473 ILE
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  888 VAL
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain B residue  485 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 76 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 53 optimal weight:    0.2980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 HIS
A 401 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 670 HIS
B 495 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.163485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.140641 restraints weight = 12594.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.144353 restraints weight = 6773.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.146766 restraints weight = 4216.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.148527 restraints weight = 2954.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.149552 restraints weight = 2273.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6396
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9046  Z= 0.171
  Angle     :  0.620   7.145  12494  Z= 0.346
  Chirality :  0.041   0.186   1438
  Planarity :  0.004   0.047   1373
  Dihedral  : 24.278 144.117   1749
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.97 %
    Favored  : 78.64 %
  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: -1.21 (0.27), residues: 905
  helix: -0.01 (0.21), residues: 635
  sheet:  None (None), residues: 0
  loop : -2.62 (0.31), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 910 
 TYR   0.014   0.001   TYR A 657 
 PHE   0.014   0.001   PHE A 118 
 TRP   0.009   0.001   TRP B 408 
 HIS   0.004   0.001   HIS B 495 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 9046)
  covalent geometry    : angle       0.62001 (12494)
  hydrogen bonds       : bond        0.04757 (  481)
  hydrogen bonds       : angle       3.95199 ( 1368)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 161
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ILE cc_start: 0.8106 (mm) cc_final: 0.7762 (mt)
REVERT: A   19 GLU cc_start: 0.7079 (tt0) cc_final: 0.6853 (tt0)
REVERT: A   72 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7494 (tm-30)
REVERT: A  288 GLU cc_start: 0.6563 (tm-30) cc_final: 0.6129 (tt0)
REVERT: A  333 LEU cc_start: 0.8052 (mt) cc_final: 0.7680 (tp)
REVERT: A  431 ARG cc_start: 0.5222 (mtp180) cc_final: 0.4501 (mtp180)
REVERT: A  443 MET cc_start: 0.7710 (tpp) cc_final: 0.7220 (tpt)
REVERT: A  641 MET cc_start: 0.6952 (tpt) cc_final: 0.6661 (tpt)
REVERT: A  692 LYS cc_start: 0.7963 (mmmt) cc_final: 0.7700 (mmmt)
REVERT: B  391 MET cc_start: 0.6451 (mmp) cc_final: 0.5950 (mmt)
REVERT: B  492 ASN cc_start: 0.7937 (t0) cc_final: 0.7583 (m-40)
  outliers start: 20
  outliers final: 15
  residues processed: 173
  average time/residue: 0.0921
  time to fit residues: 21.4793
Evaluate side-chains
  172 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 157
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain A residue  758 HIS
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  888 VAL
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain B residue  485 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 76 optimal weight:    0.6980
   chunk 93 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0170
   chunk 28 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 HIS
A 401 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.164844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.141969 restraints weight = 12741.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.145745 restraints weight = 6828.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.148286 restraints weight = 4224.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.150083 restraints weight = 2930.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.151297 restraints weight = 2225.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6362
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9046  Z= 0.153
  Angle     :  0.606   8.847  12494  Z= 0.337
  Chirality :  0.040   0.173   1438
  Planarity :  0.004   0.047   1373
  Dihedral  : 24.155 145.856   1749
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 20.05 %
    Favored  : 77.21 %
  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: -1.01 (0.27), residues: 905
  helix:  0.14 (0.21), residues: 635
  sheet:  None (None), residues: 0
  loop : -2.56 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 910 
 TYR   0.015   0.001   TYR A 657 
 PHE   0.013   0.001   PHE A 808 
 TRP   0.008   0.001   TRP A 780 
 HIS   0.004   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9046)
  covalent geometry    : angle       0.60633 (12494)
  hydrogen bonds       : bond        0.04546 (  481)
  hydrogen bonds       : angle       3.85216 ( 1368)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 167
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ILE cc_start: 0.8069 (mm) cc_final: 0.7726 (mt)
REVERT: A   19 GLU cc_start: 0.7087 (tt0) cc_final: 0.6859 (tt0)
REVERT: A   72 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7508 (tm-30)
REVERT: A  185 PHE cc_start: 0.7187 (m-80) cc_final: 0.6778 (m-10)
REVERT: A  227 MET cc_start: 0.7554 (ttm) cc_final: 0.7340 (ttm)
REVERT: A  333 LEU cc_start: 0.7945 (mt) cc_final: 0.7620 (tp)
REVERT: A  431 ARG cc_start: 0.5097 (mtp180) cc_final: 0.4429 (mtp180)
REVERT: A  443 MET cc_start: 0.7732 (tpp) cc_final: 0.7213 (tpt)
REVERT: A  692 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7684 (mmmt)
REVERT: A  852 ILE cc_start: 0.7846 (mm) cc_final: 0.7571 (mm)
REVERT: B  391 MET cc_start: 0.6421 (mmp) cc_final: 0.5948 (mmt)
REVERT: B  408 TRP cc_start: 0.5470 (p-90) cc_final: 0.5015 (p-90)
  outliers start: 23
  outliers final: 18
  residues processed: 179
  average time/residue: 0.1076
  time to fit residues: 25.7719
Evaluate side-chains
  184 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  705 ILE
Chi-restraints excluded: chain A residue  758 HIS
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  888 VAL
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain B residue  485 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 74 optimal weight:    0.1980
   chunk 23 optimal weight:    0.0470
   chunk 64 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 HIS
A 401 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN
** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 670 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.164192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.141249 restraints weight = 12681.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.144929 restraints weight = 6838.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.147447 restraints weight = 4283.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.149198 restraints weight = 3010.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.150409 restraints weight = 2291.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6378
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9046  Z= 0.163
  Angle     :  0.617   8.293  12494  Z= 0.342
  Chirality :  0.040   0.143   1438
  Planarity :  0.004   0.049   1373
  Dihedral  : 24.088 146.408   1749
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 21.96 %
    Favored  : 75.66 %
  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: -0.89 (0.27), residues: 905
  helix:  0.20 (0.21), residues: 633
  sheet:  None (None), residues: 0
  loop : -2.39 (0.32), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 910 
 TYR   0.015   0.001   TYR A 657 
 PHE   0.017   0.001   PHE A 808 
 TRP   0.006   0.001   TRP A 780 
 HIS   0.004   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 9046)
  covalent geometry    : angle       0.61745 (12494)
  hydrogen bonds       : bond        0.04542 (  481)
  hydrogen bonds       : angle       3.84413 ( 1368)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ILE cc_start: 0.8059 (mm) cc_final: 0.7720 (mt)
REVERT: A   19 GLU cc_start: 0.7060 (tt0) cc_final: 0.6841 (tt0)
REVERT: A   72 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7439 (tp30)
REVERT: A  185 PHE cc_start: 0.7132 (m-80) cc_final: 0.6719 (m-10)
REVERT: A  288 GLU cc_start: 0.6967 (pm20) cc_final: 0.6578 (pm20)
REVERT: A  333 LEU cc_start: 0.7940 (mt) cc_final: 0.7620 (tp)
REVERT: A  431 ARG cc_start: 0.4958 (mtp180) cc_final: 0.4200 (mtp180)
REVERT: A  443 MET cc_start: 0.7702 (tpp) cc_final: 0.7241 (tpt)
REVERT: A  692 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7691 (mmmt)
REVERT: A  852 ILE cc_start: 0.7919 (mm) cc_final: 0.7658 (mm)
REVERT: B  391 MET cc_start: 0.6436 (mmp) cc_final: 0.5979 (mmt)
  outliers start: 20
  outliers final: 16
  residues processed: 177
  average time/residue: 0.0957
  time to fit residues: 22.6501
Evaluate side-chains
  177 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 161
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  758 HIS
Chi-restraints excluded: chain A residue  778 VAL
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  888 VAL
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain B residue  485 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0170
   chunk 27 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 93 optimal weight:    4.9990
   chunk 67 optimal weight:    0.2980
   chunk 30 optimal weight:    0.7980
   chunk 90 optimal weight:    0.4980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
A  31 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN
** A 640 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 = 0.4147 r_free = 0.4147 target = 0.165127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.141706 restraints weight = 12638.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.145264 restraints weight = 7026.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.147788 restraints weight = 4515.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.149489 restraints weight = 3222.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.150661 restraints weight = 2513.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6362
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9046  Z= 0.147
  Angle     :  0.606   8.629  12494  Z= 0.334
  Chirality :  0.039   0.149   1438
  Planarity :  0.004   0.049   1373
  Dihedral  : 24.021 142.542   1749
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.20 %
    Favored  : 75.54 %
  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: -0.76 (0.27), residues: 905
  helix:  0.35 (0.21), residues: 629
  sheet:  None (None), residues: 0
  loop : -2.47 (0.31), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 910 
 TYR   0.014   0.001   TYR A 657 
 PHE   0.011   0.001   PHE A 354 
 TRP   0.013   0.001   TRP A 351 
 HIS   0.018   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9046)
  covalent geometry    : angle       0.60594 (12494)
  hydrogen bonds       : bond        0.04326 (  481)
  hydrogen bonds       : angle       3.78346 ( 1368)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.7577 (mttm) cc_final: 0.7292 (mttm)
REVERT: A   13 ILE cc_start: 0.8090 (mm) cc_final: 0.7749 (mt)
REVERT: A   19 GLU cc_start: 0.6999 (tt0) cc_final: 0.6785 (tt0)
REVERT: A  190 GLN cc_start: 0.7986 (mp10) cc_final: 0.7781 (mp10)
REVERT: A  333 LEU cc_start: 0.7905 (mt) cc_final: 0.7594 (tp)
REVERT: A  431 ARG cc_start: 0.4888 (mtp180) cc_final: 0.4098 (mtp180)
REVERT: A  443 MET cc_start: 0.7719 (tpp) cc_final: 0.7276 (tpt)
REVERT: A  641 MET cc_start: 0.7044 (tpt) cc_final: 0.6768 (tpt)
REVERT: A  692 LYS cc_start: 0.7908 (mmmt) cc_final: 0.7690 (mmmt)
REVERT: A  852 ILE cc_start: 0.7911 (mm) cc_final: 0.7647 (mm)
REVERT: B  391 MET cc_start: 0.6421 (mmp) cc_final: 0.5965 (mmt)
REVERT: B  408 TRP cc_start: 0.5342 (p-90) cc_final: 0.4696 (p-90)
  outliers start: 19
  outliers final: 16
  residues processed: 174
  average time/residue: 0.1046
  time to fit residues: 24.1672
Evaluate side-chains
  176 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   31 HIS
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  758 HIS
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  888 VAL
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain B residue  485 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 83 optimal weight:    0.1980
   chunk 33 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 76 optimal weight:    0.0070
   chunk 0 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0170
   chunk 71 optimal weight:    0.4980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.3036

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN
** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.166430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.143374 restraints weight = 12602.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.147150 restraints weight = 6822.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.149714 restraints weight = 4260.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.151395 restraints weight = 2994.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.152678 restraints weight = 2300.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6323
moved from start:          0.3285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9046  Z= 0.137
  Angle     :  0.603  10.173  12494  Z= 0.332
  Chirality :  0.039   0.155   1438
  Planarity :  0.004   0.052   1373
  Dihedral  : 23.919 138.162   1749
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 22.79 %
    Favored  : 75.42 %
  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: -0.61 (0.28), residues: 905
  helix:  0.46 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.42 (0.31), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 910 
 TYR   0.014   0.001   TYR A 657 
 PHE   0.011   0.001   PHE A 354 
 TRP   0.013   0.001   TRP A 351 
 HIS   0.016   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9046)
  covalent geometry    : angle       0.60301 (12494)
  hydrogen bonds       : bond        0.04126 (  481)
  hydrogen bonds       : angle       3.70882 ( 1368)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 165
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ILE cc_start: 0.8042 (mm) cc_final: 0.7709 (mt)
REVERT: A  252 ARG cc_start: 0.7096 (mtm110) cc_final: 0.6865 (mtm180)
REVERT: A  265 ARG cc_start: 0.8268 (mtp-110) cc_final: 0.7965 (ttm110)
REVERT: A  443 MET cc_start: 0.7644 (tpp) cc_final: 0.7200 (tpt)
REVERT: A  641 MET cc_start: 0.7045 (tpt) cc_final: 0.6807 (tpt)
REVERT: A  692 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7687 (mmmt)
REVERT: A  852 ILE cc_start: 0.7814 (mm) cc_final: 0.7535 (mm)
REVERT: B  391 MET cc_start: 0.6424 (mmp) cc_final: 0.5994 (mmt)
REVERT: B  492 ASN cc_start: 0.7825 (t0) cc_final: 0.7521 (m-40)
  outliers start: 15
  outliers final: 13
  residues processed: 172
  average time/residue: 0.1150
  time to fit residues: 25.9395
Evaluate side-chains
  174 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  758 HIS
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  888 VAL
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain B residue  485 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0570
   chunk 48 optimal weight:    0.0970
   chunk 30 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0870
   chunk 19 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.3474

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.166607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.143656 restraints weight = 12695.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.147477 restraints weight = 6889.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.150051 restraints weight = 4284.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.151808 restraints weight = 2979.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.152960 restraints weight = 2280.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6314
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9046  Z= 0.141
  Angle     :  0.616  10.155  12494  Z= 0.338
  Chirality :  0.039   0.155   1438
  Planarity :  0.004   0.056   1373
  Dihedral  : 23.881 137.131   1749
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 23.27 %
    Favored  : 75.06 %
  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: -0.61 (0.28), residues: 905
  helix:  0.46 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.49 (0.31), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 910 
 TYR   0.015   0.001   TYR A 657 
 PHE   0.012   0.001   PHE A 354 
 TRP   0.011   0.001   TRP A 351 
 HIS   0.007   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9046)
  covalent geometry    : angle       0.61553 (12494)
  hydrogen bonds       : bond        0.04085 (  481)
  hydrogen bonds       : angle       3.69750 ( 1368)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 158
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ILE cc_start: 0.8040 (mm) cc_final: 0.7706 (mt)
REVERT: A   72 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7352 (tm-30)
REVERT: A  185 PHE cc_start: 0.6965 (m-80) cc_final: 0.6596 (m-10)
REVERT: A  443 MET cc_start: 0.7553 (tpp) cc_final: 0.7161 (tpt)
REVERT: A  641 MET cc_start: 0.7013 (tpt) cc_final: 0.6783 (tpt)
REVERT: A  692 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7677 (mmmt)
REVERT: A  852 ILE cc_start: 0.7835 (mm) cc_final: 0.7557 (mm)
REVERT: B  391 MET cc_start: 0.6411 (mmp) cc_final: 0.6010 (mmt)
REVERT: B  492 ASN cc_start: 0.7670 (t0) cc_final: 0.7458 (m-40)
  outliers start: 14
  outliers final: 13
  residues processed: 166
  average time/residue: 0.1066
  time to fit residues: 23.5089
Evaluate side-chains
  171 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 158
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  758 HIS
Chi-restraints excluded: chain A residue  787 VAL
Chi-restraints excluded: chain A residue  816 VAL
Chi-restraints excluded: chain A residue  888 VAL
Chi-restraints excluded: chain A residue  893 LEU
Chi-restraints excluded: chain B residue  485 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 18 optimal weight:    0.4980
   chunk 34 optimal weight:    0.6980
   chunk 81 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 16 optimal weight:    0.3980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 424 GLN
A 596 ASN
** A 640 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 = 0.4146 r_free = 0.4146 target = 0.165113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.141745 restraints weight = 12589.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.145415 restraints weight = 7032.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.147893 restraints weight = 4485.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.149556 restraints weight = 3195.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.150648 restraints weight = 2504.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6364
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9046  Z= 0.160
  Angle     :  0.630   9.866  12494  Z= 0.345
  Chirality :  0.040   0.163   1438
  Planarity :  0.004   0.056   1373
  Dihedral  : 23.903 135.566   1749
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 22.91 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.27), residues: 905
  helix:  0.40 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.47 (0.31), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 910 
 TYR   0.015   0.001   TYR A 657 
 PHE   0.010   0.001   PHE A 354 
 TRP   0.019   0.001   TRP A 351 
 HIS   0.007   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 9046)
  covalent geometry    : angle       0.63029 (12494)
  hydrogen bonds       : bond        0.04274 (  481)
  hydrogen bonds       : angle       3.77320 ( 1368)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1422.56 seconds
wall clock time: 25 minutes 12.31 seconds (1512.31 seconds total)