Starting phenix.real_space_refine
on Wed Mar  4 13:13:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w84_32351/03_2026/7w84_32351.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w84_32351/03_2026/7w84_32351.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w84_32351/03_2026/7w84_32351.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w84_32351/03_2026/7w84_32351.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w84_32351/03_2026/7w84_32351.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w84_32351/03_2026/7w84_32351.map"
  }
  resolution = 3.4
  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=   0.184 sd=   0.712
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7474 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    4993      2.51       5
     N    1376      2.21       5
     O    1461      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 88 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: 7879
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7879
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 995, 7879
          Classifications: {'peptide': 995}
          Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 949}
          Chain breaks: 1
  Time building chain proxies: 1.72, per 1000 atoms: 0.22
  Number of scatterers: 7879
  At special positions: 0
  Unit cell: (81.18, 104.28, 101.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      49     16.00
     O    1461      8.00
     N    1376      7.00
     C    4993      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 728 " - pdb=" SG  CYS A 805 " distance=2.04

  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: 0.62
  Conformation dependent library (CDL) restraints added in 246.1 milliseconds
  

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1874

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 8 sheets defined
      40.1% alpha, 11.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 141 through 143
      No H-bonds generated for 'chain 'A' and resid 141 through 143'
    Processing helix  chain 'A' and resid 229 through 234
      removed outlier: 4.249A  pdb=" N   GLU A 233 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 303
    Processing helix  chain 'A' and resid 312 through 322
      removed outlier: 3.726A  pdb=" N   LEU A 322 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 335
      removed outlier: 3.534A  pdb=" N   LEU A 327 " --> pdb=" O   SER A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 359
      removed outlier: 3.502A  pdb=" N   ASN A 356 " --> pdb=" O   ALA A 352 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   MET A 357 " --> pdb=" O   HIS A 353 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   LYS A 359 " --> pdb=" O   MET A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 401
      removed outlier: 3.690A  pdb=" N   LYS A 399 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 426
      removed outlier: 3.717A  pdb=" N   LEU A 426 " --> pdb=" O   PRO A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 434
    Processing helix  chain 'A' and resid 441 through 453
      removed outlier: 3.901A  pdb=" N   HIS A 445 " --> pdb=" O   THR A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 474
    Processing helix  chain 'A' and resid 487 through 496
      removed outlier: 3.570A  pdb=" N   GLY A 496 " --> pdb=" O   ARG A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 513
    Processing helix  chain 'A' and resid 554 through 564
    Processing helix  chain 'A' and resid 627 through 636
    Processing helix  chain 'A' and resid 640 through 658
      removed outlier: 4.323A  pdb=" N   PHE A 644 " --> pdb=" O   LYS A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 671
      removed outlier: 3.965A  pdb=" N   LYS A 671 " --> pdb=" O   SER A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 686
    Processing helix  chain 'A' and resid 693 through 715
    Processing helix  chain 'A' and resid 747 through 751
    Processing helix  chain 'A' and resid 794 through 800
    Processing helix  chain 'A' and resid 816 through 820
    Processing helix  chain 'A' and resid 862 through 877
      removed outlier: 3.613A  pdb=" N   ILE A 866 " --> pdb=" O   THR A 862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 892
    Processing helix  chain 'A' and resid 899 through 913
    Processing helix  chain 'A' and resid 914 through 916
      No H-bonds generated for 'chain 'A' and resid 914 through 916'
    Processing helix  chain 'A' and resid 934 through 938
      removed outlier: 4.131A  pdb=" N   MET A 937 " --> pdb=" O   PRO A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 949 through 966
    Processing helix  chain 'A' and resid 991 through 1012
      removed outlier: 3.944A  pdb=" N   GLU A 996 " --> pdb=" O   ASP A 992 " (cutoff:3.500A)
      removed outlier: 4.940A  pdb=" N   ARG A 997 " --> pdb=" O   ALA A 993 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1023
      removed outlier: 3.800A  pdb=" N   ILE A1020 " --> pdb=" O   ARG A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1034
      removed outlier: 4.341A  pdb=" N   ARG A1034 " --> pdb=" O   VAL A1030 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1036 through 1064
      removed outlier: 3.614A  pdb=" N   CYS A1064 " --> pdb=" O   TRP A1060 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1067
      No H-bonds generated for 'chain 'A' and resid 1065 through 1067'
    Processing helix  chain 'A' and resid 1068 through 1082
      removed outlier: 3.554A  pdb=" N   HIS A1082 " --> pdb=" O   HIS A1078 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1097
    Processing helix  chain 'A' and resid 1098 through 1103
    Processing helix  chain 'A' and resid 1103 through 1110
      removed outlier: 3.636A  pdb=" N   ALA A1107 " --> pdb=" O   LEU A1103 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183
      removed outlier: 6.699A  pdb=" N   ALA A 111 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL A 135 " --> pdb=" O   ALA A 111 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   ALA A 113 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   ASP A 133 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   LEU A 115 " --> pdb=" O   SER A 131 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   SER A 131 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU A 117 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   GLY A 134 " --> pdb=" O   LYS A 151 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   LYS A 151 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 372 through 374
    Processing sheet with id=AA3, first strand: chain 'A' and resid 384 through 386
      removed outlier: 6.446A  pdb=" N   ILE A 377 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   TRP A 478 " --> pdb=" O   LEU A 465 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 536 through 538
    Processing sheet with id=AA5, first strand: chain 'A' and resid 550 through 553
      removed outlier: 6.196A  pdb=" N   GLY A 551 " --> pdb=" O   THR A 588 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 625 through 626
      removed outlier: 3.609A  pdb=" N   VAL A 626 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   ILE A 717 " --> pdb=" O   VAL A 626 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 739 through 740
      removed outlier: 8.531A  pdb=" N   VAL A 806 " --> pdb=" O   VAL A 724 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   ILE A 726 " --> pdb=" O   VAL A 806 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   PHE A 808 " --> pdb=" O   ILE A 726 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   CYS A 728 " --> pdb=" O   PHE A 808 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 744 through 745
      removed outlier: 6.814A  pdb=" N   THR A 766 " --> pdb=" O   ASP A 762 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ASP A 762 " --> pdb=" O   THR A 766 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL A 768 " --> pdb=" O   CYS A 760 " (cutoff:3.500A)

    309 hydrogen bonds defined for protein.
    855 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.19

  Time building geometry restraints manager: 0.86 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: 2539
        1.34 -     1.46: 1164
        1.46 -     1.57: 4274
        1.57 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 8052
  Sorted by residual:
  bond pdb=" CA  GLU A 252 "
       pdb=" C   GLU A 252 "
    ideal  model  delta    sigma   weight residual
    1.524  1.489  0.036 1.22e-02 6.72e+03 8.48e+00
  bond pdb=" N   ASN A1024 "
       pdb=" CA  ASN A1024 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.033 1.21e-02 6.83e+03 7.56e+00
  bond pdb=" N   ASP A 964 "
       pdb=" CA  ASP A 964 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.23e-02 6.61e+03 6.51e+00
  bond pdb=" CA  LEU A 362 "
       pdb=" C   LEU A 362 "
    ideal  model  delta    sigma   weight residual
    1.526  1.496  0.030 1.18e-02 7.18e+03 6.27e+00
  bond pdb=" N   SER A 602 "
       pdb=" CA  SER A 602 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.034 1.37e-02 5.33e+03 6.01e+00
  ... (remaining 8047 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 10622
        2.08 -     4.17: 230
        4.17 -     6.25: 25
        6.25 -     8.34: 4
        8.34 -    10.42: 2
  Bond angle restraints: 10883
  Sorted by residual:
  angle pdb=" N   ARG A 358 "
        pdb=" CA  ARG A 358 "
        pdb=" C   ARG A 358 "
      ideal   model   delta    sigma   weight residual
     111.07  100.65   10.42 1.07e+00 8.73e-01 9.48e+01
  angle pdb=" N   LEU A 251 "
        pdb=" CA  LEU A 251 "
        pdb=" C   LEU A 251 "
      ideal   model   delta    sigma   weight residual
     112.92  102.73   10.19 1.23e+00 6.61e-01 6.86e+01
  angle pdb=" N   ILE A 250 "
        pdb=" CA  ILE A 250 "
        pdb=" C   ILE A 250 "
      ideal   model   delta    sigma   weight residual
     106.21  113.52   -7.31 1.07e+00 8.73e-01 4.67e+01
  angle pdb=" CA  ILE A 250 "
        pdb=" C   ILE A 250 "
        pdb=" O   ILE A 250 "
      ideal   model   delta    sigma   weight residual
     122.63  118.63    4.00 8.70e-01 1.32e+00 2.12e+01
  angle pdb=" C   TYR A 249 "
        pdb=" N   ILE A 250 "
        pdb=" CA  ILE A 250 "
      ideal   model   delta    sigma   weight residual
     121.65  125.47   -3.82 9.40e-01 1.13e+00 1.65e+01
  ... (remaining 10878 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 4239
       17.80 -    35.60: 484
       35.60 -    53.40: 137
       53.40 -    71.20: 20
       71.20 -    89.00: 11
  Dihedral angle restraints: 4891
    sinusoidal: 1986
      harmonic: 2905
  Sorted by residual:
  dihedral pdb=" CB  CYS A 728 "
           pdb=" SG  CYS A 728 "
           pdb=" SG  CYS A 805 "
           pdb=" CB  CYS A 805 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.73   41.27     1      1.00e+01 1.00e-02 2.38e+01
  dihedral pdb=" CA  ALA A 851 "
           pdb=" C   ALA A 851 "
           pdb=" N   THR A 852 "
           pdb=" CA  THR A 852 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.21  -22.79     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ASN A 596 "
           pdb=" C   ASN A 596 "
           pdb=" N   LEU A 597 "
           pdb=" CA  LEU A 597 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.69   20.31     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 4888 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1065
       0.074 -    0.148: 119
       0.148 -    0.222: 3
       0.222 -    0.296: 3
       0.296 -    0.370: 3
  Chirality restraints: 1193
  Sorted by residual:
  chirality pdb=" CA  SER A 253 "
            pdb=" N   SER A 253 "
            pdb=" C   SER A 253 "
            pdb=" CB  SER A 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.42e+00
  chirality pdb=" CA  LEU A 251 "
            pdb=" N   LEU A 251 "
            pdb=" C   LEU A 251 "
            pdb=" CB  LEU A 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" CA  MET A 357 "
            pdb=" N   MET A 357 "
            pdb=" C   MET A 357 "
            pdb=" CB  MET A 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.22e+00
  ... (remaining 1190 not shown)

  Planarity restraints: 1405
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 249 "   -0.014 2.00e-02 2.50e+03   2.99e-02 8.93e+00
        pdb=" C   TYR A 249 "    0.052 2.00e-02 2.50e+03
        pdb=" O   TYR A 249 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ILE A 250 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 356 "   -0.012 2.00e-02 2.50e+03   2.36e-02 5.58e+00
        pdb=" C   ASN A 356 "    0.041 2.00e-02 2.50e+03
        pdb=" O   ASN A 356 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   MET A 357 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 973 "   -0.033 5.00e-02 4.00e+02   4.96e-02 3.93e+00
        pdb=" N   PRO A 974 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 974 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 974 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1402 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.57: 115
        2.57 -     3.15: 6711
        3.15 -     3.73: 12535
        3.73 -     4.32: 16181
        4.32 -     4.90: 26669
  Nonbonded interactions: 62211
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 219 "
            pdb=" CG2 VAL A 220 "
     model   vdw
     1.982 3.460
  nonbonded pdb=" O   ARG A1085 "
            pdb=" NZ  LYS A1089 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" NH2 ARG A 519 "
            pdb=" O   ILE A 565 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" OD2 ASP A 590 "
            pdb=" OG1 THR A 592 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG  SER A 754 "
            pdb=" OE2 GLU A 755 "
     model   vdw
     2.247 3.040
  ... (remaining 62206 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.900
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8053  Z= 0.224
  Angle     :  0.737  10.419  10885  Z= 0.456
  Chirality :  0.049   0.370   1193
  Planarity :  0.004   0.050   1405
  Dihedral  : 16.684  89.002   3014
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 18.13
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 12.92 %
    Favored  : 86.98 %
  Rotamer:
    Outliers :  7.85 %
    Allowed  : 20.52 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -3.60 (0.24), residues: 991
  helix: -0.59 (0.25), residues: 347
  sheet: -3.80 (0.38), residues: 101
  loop : -3.49 (0.23), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 124 
 TYR   0.013   0.001   TYR A 998 
 PHE   0.011   0.001   PHE A 576 
 TRP   0.007   0.001   TRP A1092 
 HIS   0.002   0.001   HIS A 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8052)
  covalent geometry    : angle       0.73749 (10883)
  SS BOND              : bond        0.00801 (    1)
  SS BOND              : angle       0.37686 (    2)
  hydrogen bonds       : bond        0.12715 (  309)
  hydrogen bonds       : angle       6.22740 (  855)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 261
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7120 (mm-30)
REVERT: A  337 LEU cc_start: 0.8595 (tp) cc_final: 0.8313 (tp)
REVERT: A  376 ARG cc_start: 0.8054 (mtp-110) cc_final: 0.7721 (ttm110)
REVERT: A  416 GLU cc_start: 0.8373 (tp30) cc_final: 0.8049 (tp30)
REVERT: A  489 GLU cc_start: 0.7408 (tp30) cc_final: 0.7029 (tp30)
REVERT: A  513 GLN cc_start: 0.8251 (tt0) cc_final: 0.7978 (tt0)
REVERT: A  663 GLU cc_start: 0.8266 (pp20) cc_final: 0.7785 (pp20)
REVERT: A  696 LEU cc_start: 0.8154 (tp) cc_final: 0.7848 (tp)
REVERT: A  781 LEU cc_start: 0.8054 (mt) cc_final: 0.7602 (mt)
REVERT: A  828 ASP cc_start: 0.8332 (t70) cc_final: 0.8018 (t70)
REVERT: A  867 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7789 (mm-40)
REVERT: A  874 MET cc_start: 0.7354 (ttm) cc_final: 0.7085 (ttm)
REVERT: A  889 HIS cc_start: 0.7486 (m170) cc_final: 0.7187 (m-70)
REVERT: A  914 ASP cc_start: 0.7708 (t70) cc_final: 0.7319 (t0)
REVERT: A  981 ASP cc_start: 0.8030 (t0) cc_final: 0.7797 (t0)
REVERT: A  983 GLU cc_start: 0.8545 (pp20) cc_final: 0.8189 (pp20)
REVERT: A  995 GLU cc_start: 0.8379 (tp30) cc_final: 0.7493 (tp30)
REVERT: A  999 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8007 (mm-30)
  outliers start: 67
  outliers final: 45
  residues processed: 306
  average time/residue: 0.1060
  time to fit residues: 41.7787
Evaluate side-chains
  274 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 228
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  568 ASP
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  641 ASP
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  728 CYS
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  734 LYS
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  867 GLN
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  948 ASN
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  976 CYS
Chi-restraints excluded: chain A residue  987 PHE
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain A residue 1024 ASN
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1079 VAL
Chi-restraints excluded: chain A residue 1101 THR
Chi-restraints excluded: chain A residue 1115 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 191 HIS
A 285 ASN
A 346 GLN
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 424 ASN
A 471 GLN
A 617 ASN
A 739 GLN
A 747 ASN
A 909 HIS
A1078 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.104052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.093894 restraints weight = 18789.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 3.45
r_work: 0.3274 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8053  Z= 0.154
  Angle     :  0.693  12.011  10885  Z= 0.352
  Chirality :  0.045   0.188   1193
  Planarity :  0.005   0.053   1405
  Dihedral  :  8.813  59.596   1181
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.20 %
    Favored  : 88.80 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 25.44 %
    Favored  : 68.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -2.60 (0.26), residues: 991
  helix:  0.50 (0.27), residues: 356
  sheet: -3.34 (0.39), residues: 107
  loop : -3.11 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 358 
 TYR   0.021   0.002   TYR A 291 
 PHE   0.021   0.002   PHE A 435 
 TRP   0.014   0.001   TRP A1076 
 HIS   0.007   0.001   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8052)
  covalent geometry    : angle       0.69276 (10883)
  SS BOND              : bond        0.00384 (    1)
  SS BOND              : angle       0.31164 (    2)
  hydrogen bonds       : bond        0.03733 (  309)
  hydrogen bonds       : angle       5.16357 (  855)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 246
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 TYR cc_start: 0.8381 (m-80) cc_final: 0.8135 (m-10)
REVERT: A  233 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7735 (mm-30)
REVERT: A  337 LEU cc_start: 0.8648 (tp) cc_final: 0.8366 (tp)
REVERT: A  376 ARG cc_start: 0.8569 (mtp-110) cc_final: 0.8200 (ttm110)
REVERT: A  402 SER cc_start: 0.9100 (t) cc_final: 0.8773 (m)
REVERT: A  416 GLU cc_start: 0.8548 (tp30) cc_final: 0.8248 (tp30)
REVERT: A  489 GLU cc_start: 0.7888 (tp30) cc_final: 0.7476 (tp30)
REVERT: A  497 HIS cc_start: 0.8860 (OUTLIER) cc_final: 0.8253 (t70)
REVERT: A  513 GLN cc_start: 0.8386 (tt0) cc_final: 0.8063 (tt0)
REVERT: A  514 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8810 (tt)
REVERT: A  595 PHE cc_start: 0.5699 (OUTLIER) cc_final: 0.5042 (t80)
REVERT: A  606 PHE cc_start: 0.6693 (p90) cc_final: 0.6343 (p90)
REVERT: A  736 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8454 (tm-30)
REVERT: A  828 ASP cc_start: 0.8388 (t70) cc_final: 0.8147 (t70)
REVERT: A  842 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8430 (ttpp)
REVERT: A  867 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7935 (mm-40)
REVERT: A  873 TYR cc_start: 0.9093 (t80) cc_final: 0.8869 (t80)
REVERT: A  896 LYS cc_start: 0.7711 (mtmt) cc_final: 0.7482 (mtmt)
REVERT: A  914 ASP cc_start: 0.8161 (t70) cc_final: 0.7721 (t0)
REVERT: A  981 ASP cc_start: 0.8156 (t0) cc_final: 0.7837 (t0)
REVERT: A  983 GLU cc_start: 0.8703 (pp20) cc_final: 0.8242 (pp20)
REVERT: A  995 GLU cc_start: 0.8646 (tp30) cc_final: 0.7769 (tp30)
REVERT: A  999 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8378 (mm-30)
REVERT: A 1003 GLU cc_start: 0.8343 (pp20) cc_final: 0.7976 (pp20)
  outliers start: 54
  outliers final: 38
  residues processed: 284
  average time/residue: 0.0890
  time to fit residues: 33.8046
Evaluate side-chains
  270 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 226
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  497 HIS
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  522 PHE
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  660 THR
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  728 CYS
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  736 GLU
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  790 GLU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  842 LYS
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  867 GLN
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1079 VAL
Chi-restraints excluded: chain A residue 1115 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 52 optimal weight:    6.9990
   chunk 82 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 78 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 310 HIS
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 614 ASN
A1082 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.104444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.094183 restraints weight = 18686.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 3.47
r_work: 0.3282 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8053  Z= 0.145
  Angle     :  0.704  14.720  10885  Z= 0.350
  Chirality :  0.046   0.216   1193
  Planarity :  0.005   0.054   1405
  Dihedral  :  7.880  58.128   1145
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.00 %
    Favored  : 89.00 %
  Rotamer:
    Outliers :  7.50 %
    Allowed  : 26.14 %
    Favored  : 66.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -2.31 (0.26), residues: 991
  helix:  0.75 (0.27), residues: 362
  sheet: -3.09 (0.38), residues: 129
  loop : -2.97 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 853 
 TYR   0.017   0.002   TYR A 291 
 PHE   0.022   0.002   PHE A 870 
 TRP   0.024   0.002   TRP A1076 
 HIS   0.009   0.001   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8052)
  covalent geometry    : angle       0.70364 (10883)
  SS BOND              : bond        0.00534 (    1)
  SS BOND              : angle       0.38231 (    2)
  hydrogen bonds       : bond        0.03544 (  309)
  hydrogen bonds       : angle       4.97696 (  855)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 238
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 TYR cc_start: 0.8380 (m-80) cc_final: 0.8114 (m-10)
REVERT: A  233 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7629 (mm-30)
REVERT: A  251 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7570 (mp)
REVERT: A  337 LEU cc_start: 0.8631 (tp) cc_final: 0.8347 (tp)
REVERT: A  376 ARG cc_start: 0.8516 (mtp-110) cc_final: 0.8150 (ttm110)
REVERT: A  387 LEU cc_start: 0.8892 (mt) cc_final: 0.8608 (mp)
REVERT: A  402 SER cc_start: 0.9092 (t) cc_final: 0.8761 (m)
REVERT: A  416 GLU cc_start: 0.8539 (tp30) cc_final: 0.8290 (tp30)
REVERT: A  467 PHE cc_start: 0.8480 (p90) cc_final: 0.8225 (p90)
REVERT: A  475 ASN cc_start: 0.8454 (m-40) cc_final: 0.8236 (m-40)
REVERT: A  489 GLU cc_start: 0.7897 (tp30) cc_final: 0.7479 (tp30)
REVERT: A  513 GLN cc_start: 0.8349 (tt0) cc_final: 0.8042 (tt0)
REVERT: A  514 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8837 (tt)
REVERT: A  595 PHE cc_start: 0.5801 (OUTLIER) cc_final: 0.5039 (t80)
REVERT: A  652 MET cc_start: 0.8134 (mmm) cc_final: 0.7698 (mmp)
REVERT: A  700 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7994 (mp)
REVERT: A  716 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8160 (ttpp)
REVERT: A  736 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8440 (tm-30)
REVERT: A  802 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8488 (tt)
REVERT: A  828 ASP cc_start: 0.8338 (t70) cc_final: 0.8128 (t70)
REVERT: A  842 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8351 (ttpp)
REVERT: A  867 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7951 (mm-40)
REVERT: A  874 MET cc_start: 0.8055 (ttm) cc_final: 0.7828 (ttm)
REVERT: A  914 ASP cc_start: 0.8010 (t70) cc_final: 0.7626 (t0)
REVERT: A  923 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7672 (pm20)
REVERT: A  983 GLU cc_start: 0.8729 (pp20) cc_final: 0.7794 (pm20)
REVERT: A  995 GLU cc_start: 0.8672 (tp30) cc_final: 0.7756 (tp30)
REVERT: A  999 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8419 (mm-30)
REVERT: A 1094 PHE cc_start: 0.8316 (t80) cc_final: 0.8060 (t80)
  outliers start: 64
  outliers final: 38
  residues processed: 283
  average time/residue: 0.0914
  time to fit residues: 34.6702
Evaluate side-chains
  272 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 225
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  728 CYS
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  736 GLU
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  842 LYS
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  859 HIS
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  867 GLN
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  923 GLU
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue  987 PHE
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain A residue 1024 ASN
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1079 VAL
Chi-restraints excluded: chain A residue 1101 THR
Chi-restraints excluded: chain A residue 1115 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 90 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 98 optimal weight:    0.2980
   chunk 48 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    2.8588

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

Flipped N/Q/H residues before XYZ refinement:
A 152 HIS
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 614 ASN
A 889 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.101158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.091085 restraints weight = 19109.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 3.43
r_work: 0.3231 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8053  Z= 0.223
  Angle     :  0.747  11.766  10885  Z= 0.380
  Chirality :  0.048   0.213   1193
  Planarity :  0.005   0.054   1405
  Dihedral  :  8.067  54.526   1139
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.52 %
    Favored  : 86.48 %
  Rotamer:
    Outliers :  7.97 %
    Allowed  : 28.25 %
    Favored  : 63.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -2.31 (0.26), residues: 991
  helix:  0.72 (0.27), residues: 360
  sheet: -3.24 (0.38), residues: 127
  loop : -2.89 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 712 
 TYR   0.020   0.002   TYR A 444 
 PHE   0.019   0.002   PHE A 515 
 TRP   0.043   0.002   TRP A1076 
 HIS   0.005   0.001   HIS A 859 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 8052)
  covalent geometry    : angle       0.74739 (10883)
  SS BOND              : bond        0.00702 (    1)
  SS BOND              : angle       0.39335 (    2)
  hydrogen bonds       : bond        0.03915 (  309)
  hydrogen bonds       : angle       5.25856 (  855)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 229
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 TYR cc_start: 0.8430 (m-80) cc_final: 0.8126 (m-10)
REVERT: A  233 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7649 (mm-30)
REVERT: A  251 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7554 (mp)
REVERT: A  337 LEU cc_start: 0.8619 (tp) cc_final: 0.8323 (tp)
REVERT: A  376 ARG cc_start: 0.8592 (mtp-110) cc_final: 0.8226 (ttm110)
REVERT: A  387 LEU cc_start: 0.8923 (mt) cc_final: 0.8618 (mp)
REVERT: A  402 SER cc_start: 0.9124 (t) cc_final: 0.8785 (m)
REVERT: A  416 GLU cc_start: 0.8565 (tp30) cc_final: 0.8321 (tp30)
REVERT: A  444 TYR cc_start: 0.7746 (t80) cc_final: 0.7519 (t80)
REVERT: A  480 PHE cc_start: 0.8518 (t80) cc_final: 0.8318 (t80)
REVERT: A  489 GLU cc_start: 0.7925 (tp30) cc_final: 0.7507 (tp30)
REVERT: A  514 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8926 (tt)
REVERT: A  534 ASP cc_start: 0.7801 (p0) cc_final: 0.7598 (p0)
REVERT: A  595 PHE cc_start: 0.6120 (OUTLIER) cc_final: 0.5519 (t80)
REVERT: A  620 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7437 (pmmt)
REVERT: A  654 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7424 (tm-30)
REVERT: A  658 MET cc_start: 0.7762 (ptm) cc_final: 0.7469 (ptm)
REVERT: A  696 LEU cc_start: 0.8218 (tp) cc_final: 0.7930 (tp)
REVERT: A  716 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8646 (ttpp)
REVERT: A  781 LEU cc_start: 0.8479 (mt) cc_final: 0.8064 (mt)
REVERT: A  798 ASP cc_start: 0.8595 (t0) cc_final: 0.8369 (m-30)
REVERT: A  828 ASP cc_start: 0.8418 (t70) cc_final: 0.8174 (t0)
REVERT: A  842 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8315 (ttpp)
REVERT: A  867 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7936 (mm-40)
REVERT: A  874 MET cc_start: 0.8200 (ttm) cc_final: 0.7953 (ttm)
REVERT: A  914 ASP cc_start: 0.8087 (t70) cc_final: 0.7703 (t0)
REVERT: A  923 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7731 (pm20)
REVERT: A  981 ASP cc_start: 0.8264 (t0) cc_final: 0.7958 (t0)
REVERT: A  983 GLU cc_start: 0.8740 (pp20) cc_final: 0.8349 (pp20)
REVERT: A  995 GLU cc_start: 0.8701 (tp30) cc_final: 0.7844 (tp30)
REVERT: A  999 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8466 (mm-30)
REVERT: A 1003 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8056 (pp20)
  outliers start: 68
  outliers final: 51
  residues processed: 271
  average time/residue: 0.0879
  time to fit residues: 32.1925
Evaluate side-chains
  280 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 221
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  497 HIS
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  522 PHE
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  620 LYS
Chi-restraints excluded: chain A residue  646 SER
Chi-restraints excluded: chain A residue  671 LYS
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  728 CYS
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  842 LYS
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  859 HIS
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  867 GLN
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  923 GLU
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  987 PHE
Chi-restraints excluded: chain A residue 1003 GLU
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain A residue 1019 GLU
Chi-restraints excluded: chain A residue 1024 ASN
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1074 SER
Chi-restraints excluded: chain A residue 1101 THR
Chi-restraints excluded: chain A residue 1102 LEU
Chi-restraints excluded: chain A residue 1115 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 94 optimal weight:    0.4980
   chunk 3 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 86 optimal weight:    6.9990
   chunk 82 optimal weight:    0.6980
   chunk 67 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 85 optimal weight:    5.9990
   overall best weight:    1.4182

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.103891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.093641 restraints weight = 18956.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 3.51
r_work: 0.3277 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8053  Z= 0.144
  Angle     :  0.695  12.438  10885  Z= 0.349
  Chirality :  0.045   0.196   1193
  Planarity :  0.005   0.054   1405
  Dihedral  :  7.583  56.583   1136
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.30 %
    Favored  : 88.70 %
  Rotamer:
    Outliers :  7.50 %
    Allowed  : 29.78 %
    Favored  : 62.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -2.04 (0.26), residues: 991
  helix:  0.94 (0.27), residues: 360
  sheet: -2.92 (0.39), residues: 132
  loop : -2.77 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 712 
 TYR   0.025   0.002   TYR A 873 
 PHE   0.019   0.002   PHE A 515 
 TRP   0.050   0.002   TRP A1076 
 HIS   0.003   0.001   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8052)
  covalent geometry    : angle       0.69460 (10883)
  SS BOND              : bond        0.00521 (    1)
  SS BOND              : angle       1.69415 (    2)
  hydrogen bonds       : bond        0.03486 (  309)
  hydrogen bonds       : angle       5.01994 (  855)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 240
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 TYR cc_start: 0.8421 (m-80) cc_final: 0.8157 (m-10)
REVERT: A  189 ARG cc_start: 0.8654 (mtt180) cc_final: 0.8362 (mtt90)
REVERT: A  233 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7714 (mm-30)
REVERT: A  337 LEU cc_start: 0.8626 (tp) cc_final: 0.8349 (tp)
REVERT: A  376 ARG cc_start: 0.8554 (mtp-110) cc_final: 0.8208 (ttm110)
REVERT: A  387 LEU cc_start: 0.8911 (mt) cc_final: 0.8614 (mp)
REVERT: A  402 SER cc_start: 0.9090 (t) cc_final: 0.8768 (m)
REVERT: A  416 GLU cc_start: 0.8529 (tp30) cc_final: 0.8325 (tp30)
REVERT: A  489 GLU cc_start: 0.7942 (tp30) cc_final: 0.7528 (tp30)
REVERT: A  595 PHE cc_start: 0.5754 (OUTLIER) cc_final: 0.4901 (t80)
REVERT: A  614 ASN cc_start: 0.8615 (m-40) cc_final: 0.8210 (m-40)
REVERT: A  654 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7431 (tm-30)
REVERT: A  658 MET cc_start: 0.7562 (ptm) cc_final: 0.7303 (ptm)
REVERT: A  716 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8559 (ttpp)
REVERT: A  736 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8463 (tm-30)
REVERT: A  781 LEU cc_start: 0.8324 (mt) cc_final: 0.7923 (mt)
REVERT: A  798 ASP cc_start: 0.8511 (t0) cc_final: 0.8287 (m-30)
REVERT: A  828 ASP cc_start: 0.8385 (t70) cc_final: 0.8183 (t0)
REVERT: A  842 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8265 (ttpp)
REVERT: A  867 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7958 (mm-40)
REVERT: A  914 ASP cc_start: 0.7938 (t70) cc_final: 0.7585 (t0)
REVERT: A  923 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7657 (pm20)
REVERT: A  983 GLU cc_start: 0.8645 (pp20) cc_final: 0.8233 (pp20)
REVERT: A  995 GLU cc_start: 0.8661 (tp30) cc_final: 0.7787 (tp30)
REVERT: A  999 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8472 (mm-30)
REVERT: A 1096 TRP cc_start: 0.8295 (m100) cc_final: 0.7924 (m100)
  outliers start: 64
  outliers final: 47
  residues processed: 279
  average time/residue: 0.0897
  time to fit residues: 33.6892
Evaluate side-chains
  284 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 232
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  498 PHE
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  522 PHE
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  646 SER
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  728 CYS
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  736 GLU
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  842 LYS
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  859 HIS
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  867 GLN
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  923 GLU
Chi-restraints excluded: chain A residue  950 VAL
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  987 PHE
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain A residue 1024 ASN
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1079 VAL
Chi-restraints excluded: chain A residue 1101 THR
Chi-restraints excluded: chain A residue 1115 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 76 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0470
   chunk 7 optimal weight:    8.9990
   chunk 71 optimal weight:    0.7980
   chunk 83 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.6680

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** 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 = 0.3604 r_free = 0.3604 target = 0.106945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.096596 restraints weight = 18721.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 3.51
r_work: 0.3323 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8053  Z= 0.123
  Angle     :  0.713  16.881  10885  Z= 0.347
  Chirality :  0.045   0.194   1193
  Planarity :  0.004   0.055   1405
  Dihedral  :  7.282  59.212   1134
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.49 %
    Favored  : 90.51 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 32.00 %
    Favored  : 61.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -1.83 (0.27), residues: 991
  helix:  1.11 (0.27), residues: 354
  sheet: -2.90 (0.41), residues: 122
  loop : -2.59 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 712 
 TYR   0.028   0.002   TYR A 873 
 PHE   0.017   0.002   PHE A 515 
 TRP   0.057   0.002   TRP A1076 
 HIS   0.003   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8052)
  covalent geometry    : angle       0.71278 (10883)
  SS BOND              : bond        0.00281 (    1)
  SS BOND              : angle       1.11615 (    2)
  hydrogen bonds       : bond        0.03247 (  309)
  hydrogen bonds       : angle       4.84487 (  855)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 237
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 TYR cc_start: 0.8351 (m-80) cc_final: 0.8066 (m-10)
REVERT: A  189 ARG cc_start: 0.8618 (mtt180) cc_final: 0.8321 (mtt90)
REVERT: A  233 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7688 (mm-30)
REVERT: A  337 LEU cc_start: 0.8642 (tp) cc_final: 0.8361 (tp)
REVERT: A  376 ARG cc_start: 0.8476 (mtp-110) cc_final: 0.8137 (ttm110)
REVERT: A  387 LEU cc_start: 0.8831 (mt) cc_final: 0.8563 (mp)
REVERT: A  402 SER cc_start: 0.9056 (t) cc_final: 0.8769 (m)
REVERT: A  429 ARG cc_start: 0.8171 (ptp90) cc_final: 0.7905 (ptt-90)
REVERT: A  489 GLU cc_start: 0.8026 (tp30) cc_final: 0.7579 (tp30)
REVERT: A  595 PHE cc_start: 0.5397 (OUTLIER) cc_final: 0.4464 (t80)
REVERT: A  614 ASN cc_start: 0.8564 (m-40) cc_final: 0.8223 (m-40)
REVERT: A  654 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7403 (tm-30)
REVERT: A  658 MET cc_start: 0.7354 (ptm) cc_final: 0.7119 (ptm)
REVERT: A  736 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8460 (tm-30)
REVERT: A  798 ASP cc_start: 0.8465 (t0) cc_final: 0.8254 (m-30)
REVERT: A  828 ASP cc_start: 0.8401 (t70) cc_final: 0.8173 (t70)
REVERT: A  914 ASP cc_start: 0.7719 (t70) cc_final: 0.7421 (t0)
REVERT: A  923 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7636 (pm20)
REVERT: A  983 GLU cc_start: 0.8574 (pp20) cc_final: 0.8162 (pp20)
REVERT: A  995 GLU cc_start: 0.8629 (tp30) cc_final: 0.7899 (tp30)
REVERT: A  999 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8311 (mm-30)
REVERT: A 1003 GLU cc_start: 0.8323 (pp20) cc_final: 0.8113 (pp20)
  outliers start: 57
  outliers final: 42
  residues processed: 271
  average time/residue: 0.0880
  time to fit residues: 31.9757
Evaluate side-chains
  269 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 224
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  498 PHE
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  646 SER
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  728 CYS
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  736 GLU
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  859 HIS
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  923 GLU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  987 PHE
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1079 VAL
Chi-restraints excluded: chain A residue 1101 THR
Chi-restraints excluded: chain A residue 1102 LEU
Chi-restraints excluded: chain A residue 1115 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 85 optimal weight:    0.4980
   chunk 23 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   chunk 96 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 18 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 471 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 = 0.3584 r_free = 0.3584 target = 0.105582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.095198 restraints weight = 18917.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 3.53
r_work: 0.3301 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8053  Z= 0.148
  Angle     :  0.735  14.589  10885  Z= 0.359
  Chirality :  0.046   0.198   1193
  Planarity :  0.005   0.054   1405
  Dihedral  :  6.851  58.906   1123
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  7.27 %
    Allowed  : 32.12 %
    Favored  : 60.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -1.86 (0.27), residues: 991
  helix:  1.00 (0.27), residues: 362
  sheet: -2.89 (0.40), residues: 125
  loop : -2.59 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 712 
 TYR   0.030   0.002   TYR A 873 
 PHE   0.018   0.002   PHE A 515 
 TRP   0.037   0.002   TRP A1076 
 HIS   0.004   0.001   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8052)
  covalent geometry    : angle       0.73495 (10883)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       1.24090 (    2)
  hydrogen bonds       : bond        0.03492 (  309)
  hydrogen bonds       : angle       4.87142 (  855)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 230
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 TYR cc_start: 0.8360 (m-80) cc_final: 0.8066 (m-10)
REVERT: A  189 ARG cc_start: 0.8710 (mtt180) cc_final: 0.8469 (mtt90)
REVERT: A  233 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7691 (mm-30)
REVERT: A  337 LEU cc_start: 0.8647 (tp) cc_final: 0.8354 (tp)
REVERT: A  376 ARG cc_start: 0.8510 (mtp-110) cc_final: 0.8170 (ttm110)
REVERT: A  387 LEU cc_start: 0.8840 (mt) cc_final: 0.8577 (mp)
REVERT: A  402 SER cc_start: 0.9036 (t) cc_final: 0.8742 (m)
REVERT: A  489 GLU cc_start: 0.8033 (tp30) cc_final: 0.7590 (tp30)
REVERT: A  577 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7639 (tm-30)
REVERT: A  595 PHE cc_start: 0.5530 (OUTLIER) cc_final: 0.4642 (t80)
REVERT: A  614 ASN cc_start: 0.8576 (m-40) cc_final: 0.8124 (m-40)
REVERT: A  620 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7343 (pmmt)
REVERT: A  654 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7464 (tm-30)
REVERT: A  658 MET cc_start: 0.7563 (ptm) cc_final: 0.7346 (ptm)
REVERT: A  736 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8431 (tm-30)
REVERT: A  781 LEU cc_start: 0.8274 (mt) cc_final: 0.7885 (mt)
REVERT: A  828 ASP cc_start: 0.8450 (t70) cc_final: 0.8178 (t70)
REVERT: A  829 LEU cc_start: 0.8460 (mt) cc_final: 0.8199 (mt)
REVERT: A  914 ASP cc_start: 0.7712 (t70) cc_final: 0.7433 (t0)
REVERT: A  923 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7658 (pm20)
REVERT: A  983 GLU cc_start: 0.8598 (pp20) cc_final: 0.8225 (pp20)
REVERT: A  995 GLU cc_start: 0.8663 (tp30) cc_final: 0.8163 (tp30)
REVERT: A  999 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8516 (mm-30)
REVERT: A 1003 GLU cc_start: 0.8329 (pp20) cc_final: 0.8027 (pp20)
  outliers start: 62
  outliers final: 48
  residues processed: 268
  average time/residue: 0.0938
  time to fit residues: 33.6983
Evaluate side-chains
  276 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 224
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  498 PHE
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  522 PHE
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain A residue  620 LYS
Chi-restraints excluded: chain A residue  646 SER
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain A residue  728 CYS
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  736 GLU
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  805 CYS
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  859 HIS
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  923 GLU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  987 PHE
Chi-restraints excluded: chain A residue 1019 GLU
Chi-restraints excluded: chain A residue 1024 ASN
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1079 VAL
Chi-restraints excluded: chain A residue 1101 THR
Chi-restraints excluded: chain A residue 1102 LEU
Chi-restraints excluded: chain A residue 1115 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   chunk 72 optimal weight:    5.9990
   chunk 96 optimal weight:    0.0470
   chunk 69 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.6882

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN
A 867 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.108000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.097590 restraints weight = 18904.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 3.55
r_work: 0.3341 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8053  Z= 0.129
  Angle     :  0.752  17.152  10885  Z= 0.362
  Chirality :  0.046   0.205   1193
  Planarity :  0.004   0.054   1405
  Dihedral  :  6.759  58.372   1123
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.28 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 33.06 %
    Favored  : 60.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -1.84 (0.26), residues: 991
  helix:  0.92 (0.27), residues: 360
  sheet: -2.75 (0.41), residues: 124
  loop : -2.51 (0.26), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 712 
 TYR   0.024   0.002   TYR A 444 
 PHE   0.043   0.002   PHE A1094 
 TRP   0.066   0.003   TRP A1076 
 HIS   0.003   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8052)
  covalent geometry    : angle       0.75199 (10883)
  SS BOND              : bond        0.00275 (    1)
  SS BOND              : angle       1.16415 (    2)
  hydrogen bonds       : bond        0.03334 (  309)
  hydrogen bonds       : angle       4.85377 (  855)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 231
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  186 TYR cc_start: 0.8416 (m-80) cc_final: 0.8020 (m-10)
REVERT: A  226 THR cc_start: 0.9137 (m) cc_final: 0.8900 (t)
REVERT: A  233 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7671 (mm-30)
REVERT: A  337 LEU cc_start: 0.8653 (tp) cc_final: 0.8383 (tp)
REVERT: A  376 ARG cc_start: 0.8440 (mtp-110) cc_final: 0.8054 (ttm110)
REVERT: A  387 LEU cc_start: 0.8779 (mt) cc_final: 0.8520 (mp)
REVERT: A  489 GLU cc_start: 0.8028 (tp30) cc_final: 0.7589 (tp30)
REVERT: A  577 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7570 (tm-30)
REVERT: A  595 PHE cc_start: 0.5509 (OUTLIER) cc_final: 0.4524 (t80)
REVERT: A  614 ASN cc_start: 0.8539 (m-40) cc_final: 0.8192 (m-40)
REVERT: A  620 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7239 (pmmt)
REVERT: A  654 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7421 (tm-30)
REVERT: A  736 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8434 (tm-30)
REVERT: A  793 TYR cc_start: 0.7995 (t80) cc_final: 0.7684 (t80)
REVERT: A  828 ASP cc_start: 0.8449 (t70) cc_final: 0.8149 (t70)
REVERT: A  829 LEU cc_start: 0.8421 (mt) cc_final: 0.8209 (mt)
REVERT: A  914 ASP cc_start: 0.7538 (t70) cc_final: 0.7280 (t0)
REVERT: A  923 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7648 (pm20)
REVERT: A  983 GLU cc_start: 0.8543 (pp20) cc_final: 0.8182 (pp20)
REVERT: A  995 GLU cc_start: 0.8654 (tp30) cc_final: 0.8208 (tp30)
REVERT: A  999 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8528 (mm-30)
  outliers start: 54
  outliers final: 40
  residues processed: 262
  average time/residue: 0.0888
  time to fit residues: 31.1166
Evaluate side-chains
  265 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 221
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  620 LYS
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain A residue  728 CYS
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  736 GLU
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  867 GLN
Chi-restraints excluded: chain A residue  887 LEU
Chi-restraints excluded: chain A residue  923 GLU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue 1019 GLU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1079 VAL
Chi-restraints excluded: chain A residue 1101 THR
Chi-restraints excluded: chain A residue 1115 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 48 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 78 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 497 HIS
A 596 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.105762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.095395 restraints weight = 18732.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 3.49
r_work: 0.3309 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8053  Z= 0.166
  Angle     :  0.772  13.797  10885  Z= 0.377
  Chirality :  0.047   0.300   1193
  Planarity :  0.005   0.054   1405
  Dihedral  :  6.925  58.333   1123
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.40 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 34.23 %
    Favored  : 59.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -1.84 (0.26), residues: 991
  helix:  0.87 (0.27), residues: 360
  sheet: -2.73 (0.42), residues: 118
  loop : -2.50 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 144 
 TYR   0.023   0.002   TYR A 444 
 PHE   0.048   0.002   PHE A1094 
 TRP   0.059   0.003   TRP A1076 
 HIS   0.019   0.001   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8052)
  covalent geometry    : angle       0.77184 (10883)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       1.12123 (    2)
  hydrogen bonds       : bond        0.03774 (  309)
  hydrogen bonds       : angle       4.97429 (  855)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 222
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  186 TYR cc_start: 0.8469 (m-80) cc_final: 0.7947 (m-10)
REVERT: A  226 THR cc_start: 0.9125 (m) cc_final: 0.8868 (t)
REVERT: A  233 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7667 (mm-30)
REVERT: A  337 LEU cc_start: 0.8673 (tp) cc_final: 0.8384 (tp)
REVERT: A  376 ARG cc_start: 0.8488 (mtp-110) cc_final: 0.8097 (ttm110)
REVERT: A  387 LEU cc_start: 0.8811 (mt) cc_final: 0.8561 (mp)
REVERT: A  489 GLU cc_start: 0.8043 (tp30) cc_final: 0.7595 (tp30)
REVERT: A  511 MET cc_start: 0.7869 (ptp) cc_final: 0.7309 (mtm)
REVERT: A  577 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7519 (tm-30)
REVERT: A  595 PHE cc_start: 0.5514 (OUTLIER) cc_final: 0.4508 (t80)
REVERT: A  614 ASN cc_start: 0.8557 (m-40) cc_final: 0.8198 (m-40)
REVERT: A  620 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7268 (pmmt)
REVERT: A  654 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7418 (tm-30)
REVERT: A  658 MET cc_start: 0.7356 (ptm) cc_final: 0.6994 (ptm)
REVERT: A  736 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8409 (tm-30)
REVERT: A  789 LEU cc_start: 0.8577 (mt) cc_final: 0.8052 (pp)
REVERT: A  828 ASP cc_start: 0.8443 (t70) cc_final: 0.8131 (t0)
REVERT: A  829 LEU cc_start: 0.8486 (mt) cc_final: 0.8164 (mt)
REVERT: A  914 ASP cc_start: 0.7666 (t70) cc_final: 0.7397 (t0)
REVERT: A  923 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7724 (pm20)
REVERT: A  983 GLU cc_start: 0.8570 (pp20) cc_final: 0.8261 (pp20)
REVERT: A  995 GLU cc_start: 0.8671 (tp30) cc_final: 0.7945 (tp30)
REVERT: A  999 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8404 (mm-30)
REVERT: A 1044 ASP cc_start: 0.8719 (t0) cc_final: 0.8484 (t0)
  outliers start: 53
  outliers final: 45
  residues processed: 254
  average time/residue: 0.0804
  time to fit residues: 27.6443
Evaluate side-chains
  265 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 216
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  620 LYS
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  728 CYS
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  736 GLU
Chi-restraints excluded: chain A residue  746 LYS
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  859 HIS
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  923 GLU
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue 1019 GLU
Chi-restraints excluded: chain A residue 1024 ASN
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1074 SER
Chi-restraints excluded: chain A residue 1079 VAL
Chi-restraints excluded: chain A residue 1101 THR
Chi-restraints excluded: chain A residue 1115 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 7 optimal weight:    9.9990
   chunk 93 optimal weight:    0.0470
   chunk 78 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   overall best weight:    3.0086

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.101954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.091833 restraints weight = 18908.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 3.46
r_work: 0.3247 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8053  Z= 0.244
  Angle     :  0.862  18.688  10885  Z= 0.428
  Chirality :  0.049   0.210   1193
  Planarity :  0.005   0.054   1405
  Dihedral  :  7.393  59.433   1123
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 17.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.92 %
    Favored  : 87.08 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 34.23 %
    Favored  : 59.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -2.09 (0.26), residues: 991
  helix:  0.62 (0.27), residues: 359
  sheet: -2.94 (0.41), residues: 120
  loop : -2.58 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 144 
 TYR   0.024   0.003   TYR A 291 
 PHE   0.040   0.003   PHE A 870 
 TRP   0.063   0.003   TRP A1076 
 HIS   0.006   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 ( 8052)
  covalent geometry    : angle       0.86157 (10883)
  SS BOND              : bond        0.00494 (    1)
  SS BOND              : angle       1.20385 (    2)
  hydrogen bonds       : bond        0.04362 (  309)
  hydrogen bonds       : angle       5.38046 (  855)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 215
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 TYR cc_start: 0.8485 (m-80) cc_final: 0.7870 (m-10)
REVERT: A  233 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7739 (mm-30)
REVERT: A  337 LEU cc_start: 0.8654 (tp) cc_final: 0.8369 (tp)
REVERT: A  376 ARG cc_start: 0.8580 (mtp-110) cc_final: 0.8193 (ttm110)
REVERT: A  387 LEU cc_start: 0.8917 (mt) cc_final: 0.8654 (mp)
REVERT: A  402 SER cc_start: 0.9068 (t) cc_final: 0.8768 (m)
REVERT: A  489 GLU cc_start: 0.8044 (tp30) cc_final: 0.7586 (tp30)
REVERT: A  577 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7602 (tm-30)
REVERT: A  595 PHE cc_start: 0.5910 (OUTLIER) cc_final: 0.4796 (t80)
REVERT: A  614 ASN cc_start: 0.8693 (m-40) cc_final: 0.8319 (m-40)
REVERT: A  620 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7377 (pmmt)
REVERT: A  654 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7477 (tm-30)
REVERT: A  658 MET cc_start: 0.7587 (ptm) cc_final: 0.7291 (ptm)
REVERT: A  789 LEU cc_start: 0.8619 (mt) cc_final: 0.8123 (pp)
REVERT: A  828 ASP cc_start: 0.8424 (t70) cc_final: 0.8184 (t0)
REVERT: A  983 GLU cc_start: 0.8687 (pp20) cc_final: 0.8441 (pp20)
REVERT: A  995 GLU cc_start: 0.8636 (tp30) cc_final: 0.8391 (tp30)
REVERT: A  999 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8625 (mm-30)
  outliers start: 51
  outliers final: 45
  residues processed: 245
  average time/residue: 0.0896
  time to fit residues: 29.6245
Evaluate side-chains
  259 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 212
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  249 TYR
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  522 PHE
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  620 LYS
Chi-restraints excluded: chain A residue  646 SER
Chi-restraints excluded: chain A residue  671 LYS
Chi-restraints excluded: chain A residue  692 SER
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  728 CYS
Chi-restraints excluded: chain A residue  730 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue 1019 GLU
Chi-restraints excluded: chain A residue 1024 ASN
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1074 SER
Chi-restraints excluded: chain A residue 1079 VAL
Chi-restraints excluded: chain A residue 1101 THR
Chi-restraints excluded: chain A residue 1115 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 42 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 364 ASN
A 424 ASN
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN
A 867 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.106467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.096040 restraints weight = 18878.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 3.55
r_work: 0.3316 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8053  Z= 0.153
  Angle     :  0.809  14.027  10885  Z= 0.399
  Chirality :  0.047   0.214   1193
  Planarity :  0.005   0.054   1405
  Dihedral  :  7.054  58.880   1123
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 35.17 %
    Favored  : 59.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -1.94 (0.26), residues: 991
  helix:  0.77 (0.27), residues: 358
  sheet: -2.66 (0.41), residues: 127
  loop : -2.54 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 144 
 TYR   0.020   0.002   TYR A 291 
 PHE   0.037   0.002   PHE A 870 
 TRP   0.071   0.003   TRP A1076 
 HIS   0.004   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8052)
  covalent geometry    : angle       0.80900 (10883)
  SS BOND              : bond        0.00379 (    1)
  SS BOND              : angle       1.58291 (    2)
  hydrogen bonds       : bond        0.03919 (  309)
  hydrogen bonds       : angle       5.16028 (  855)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1677.69 seconds
wall clock time: 29 minutes 30.98 seconds (1770.98 seconds total)