Starting phenix.real_space_refine
on Tue Mar  3 15:37:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nus_0521/03_2026/6nus_0521.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nus_0521/03_2026/6nus_0521.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nus_0521/03_2026/6nus_0521.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nus_0521/03_2026/6nus_0521.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nus_0521/03_2026/6nus_0521.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nus_0521/03_2026/6nus_0521.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      54      5.16       5
     C    4235      2.51       5
     N    1115      2.21       5
     O    1226      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s

  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: 6632
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 715, 5767
          Classifications: {'peptide': 715}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 689}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 863
          Classifications: {'peptide': 112}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1481  SG  CYS A 301      37.503  61.634  35.610  1.00 36.78           S
  ATOM   1522  SG  CYS A 306      37.698  60.632  32.501  1.00 62.98           S
  ATOM   1554  SG  CYS A 310      41.314  60.514  34.574  1.00 33.81           S
  ATOM   2658  SG  CYS A 487      19.463  58.580  43.739  1.00 37.60           S
  ATOM   3783  SG  CYS A 645      18.191  58.310  40.576  1.00 36.07           S
  ATOM   3789  SG  CYS A 646      21.574  60.826  41.973  1.00 36.63           S

  Time building chain proxies: 1.45, per 1000 atoms: 0.22
  Number of scatterers: 6632
  At special positions: 0
  Unit cell: (86.25, 93.15, 97.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      54     16.00
     O    1226      8.00
     N    1115      7.00
     C    4235      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 240.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 301 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 310 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 306 "
        pdb="ZN    ZN A1001 " - pdb=" ND1 HIS A 295 "
      pdb="  ZN A1002 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 645 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 487 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 646 "
        pdb="ZN    ZN A1002 " - pdb=" ND1 HIS A 642 "
      Number of angles added : 6


  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1584

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 7 sheets defined
      52.4% alpha, 13.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 133
    Processing helix  chain 'A' and resid 139 through 149
    Processing helix  chain 'A' and resid 153 through 159
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 178 through 199
    Processing helix  chain 'A' and resid 234 through 242
    Processing helix  chain 'A' and resid 243 through 245
      No H-bonds generated for 'chain 'A' and resid 243 through 245'
    Processing helix  chain 'A' and resid 251 through 256
      removed outlier: 3.763A  pdb=" N   SER A 255 " --> pdb=" O   ALA A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 287
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.517A  pdb=" N   ILE A 307 " --> pdb=" O   ASP A 303 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE A 313 " --> pdb=" O   HIS A 309 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LEU A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 321
      No H-bonds generated for 'chain 'A' and resid 319 through 321'
    Processing helix  chain 'A' and resid 367 through 376
    Processing helix  chain 'A' and resid 378 through 383
    Processing helix  chain 'A' and resid 416 through 425
    Processing helix  chain 'A' and resid 465 through 479
      removed outlier: 3.505A  pdb=" N   PHE A 471 " --> pdb=" O   ARG A 467 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 493
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 512 through 517
    Processing helix  chain 'A' and resid 520 through 531
    Processing helix  chain 'A' and resid 561 through 581
      removed outlier: 5.213A  pdb=" N   THR A 567 " --> pdb=" O   CYS A 563 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   GLN A 570 " --> pdb=" O   MET A 566 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   LYS A 574 " --> pdb=" O   GLN A 570 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   LEU A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 607
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 640 through 642
      No H-bonds generated for 'chain 'A' and resid 640 through 642'
    Processing helix  chain 'A' and resid 647 through 663
    Processing helix  chain 'A' and resid 686 through 709
      removed outlier: 4.206A  pdb=" N   SER A 692 " --> pdb=" O   ALA A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 715
      removed outlier: 3.804A  pdb=" N   ILE A 715 " --> pdb=" O   GLY A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 729
    Processing helix  chain 'A' and resid 738 through 752
    Processing helix  chain 'A' and resid 768 through 772
    Processing helix  chain 'A' and resid 778 through 790
    Processing helix  chain 'A' and resid 795 through 799
    Processing helix  chain 'A' and resid 833 through 840
    Processing helix  chain 'A' and resid 855 through 867
    Processing helix  chain 'A' and resid 868 through 872
    Processing helix  chain 'A' and resid 874 through 891
      removed outlier: 4.068A  pdb=" N   VAL A 880 " --> pdb=" O   GLU A 876 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   PHE A 881 " --> pdb=" O   TYR A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 910 through 915
    Processing helix  chain 'A' and resid 916 through 918
      No H-bonds generated for 'chain 'A' and resid 916 through 918'
    Processing helix  chain 'B' and resid 81 through 99
    Processing helix  chain 'B' and resid 100 through 109
    Processing helix  chain 'B' and resid 120 through 125
    Processing helix  chain 'B' and resid 134 through 140
    Processing helix  chain 'B' and resid 168 through 172
    Processing helix  chain 'B' and resid 176 through 180
    Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 224
      removed outlier: 6.589A  pdb=" N   ILE A 201 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   ILE A 233 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   GLY A 203 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 355
      removed outlier: 6.533A  pdb=" N   VAL A 335 " --> pdb=" O   PRO A 339 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   VAL A 341 " --> pdb=" O   ILE A 333 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ILE A 333 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 5.631A  pdb=" N   SER A 343 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ARG A 331 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLY A 345 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 390
      removed outlier: 6.281A  pdb=" N   LEU A 387 " --> pdb=" O   MET B 129 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   VAL B 131 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LEU A 389 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ILE B 185 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   VAL B 159 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   THR B 187 " --> pdb=" O   GLN B 157 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 390
      removed outlier: 6.281A  pdb=" N   LEU A 387 " --> pdb=" O   MET B 129 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   VAL B 131 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LEU A 389 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ILE B 185 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   VAL B 159 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   THR B 187 " --> pdb=" O   GLN B 157 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   VAL B 159 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 400
      removed outlier: 6.189A  pdb=" N   SER A 397 " --> pdb=" O   VAL A 675 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   VAL A 675 " --> pdb=" O   SER A 397 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 753 through 758
    Processing sheet with id=AA7, first strand: chain 'A' and resid 816 through 821

    319 hydrogen bonds defined for protein.
    864 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: 0.98

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1232
        1.32 -     1.45: 1957
        1.45 -     1.58: 3498
        1.58 -     1.70: 15
        1.70 -     1.83: 81
  Bond restraints: 6783
  Sorted by residual:
  bond pdb=" CB  TYR A 884 "
       pdb=" CG  TYR A 884 "
    ideal  model  delta    sigma   weight residual
    1.512  1.424  0.088 2.20e-02 2.07e+03 1.60e+01
  bond pdb=" NE  ARG A 365 "
       pdb=" CZ  ARG A 365 "
    ideal  model  delta    sigma   weight residual
    1.326  1.370 -0.044 1.10e-02 8.26e+03 1.58e+01
  bond pdb=" CB  ILE B 107 "
       pdb=" CG1 ILE B 107 "
    ideal  model  delta    sigma   weight residual
    1.530  1.609 -0.079 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" CB  LEU B  91 "
       pdb=" CG  LEU B  91 "
    ideal  model  delta    sigma   weight residual
    1.530  1.606 -0.076 2.00e-02 2.50e+03 1.43e+01
  bond pdb=" NE1 TRP A 290 "
       pdb=" CE2 TRP A 290 "
    ideal  model  delta    sigma   weight residual
    1.370  1.329  0.041 1.10e-02 8.26e+03 1.38e+01
  ... (remaining 6778 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 7482
        1.86 -     3.72: 1410
        3.72 -     5.58: 266
        5.58 -     7.44: 43
        7.44 -     9.30: 9
  Bond angle restraints: 9210
  Sorted by residual:
  angle pdb=" C   ASP A 377 "
        pdb=" N   PRO A 378 "
        pdb=" CA  PRO A 378 "
      ideal   model   delta    sigma   weight residual
     119.56  127.07   -7.51 1.02e+00 9.61e-01 5.42e+01
  angle pdb=" C   MET A 626 "
        pdb=" N   PRO A 627 "
        pdb=" CA  PRO A 627 "
      ideal   model   delta    sigma   weight residual
     119.78  127.04   -7.26 1.03e+00 9.43e-01 4.96e+01
  angle pdb=" C   ASN A 168 "
        pdb=" N   PRO A 169 "
        pdb=" CA  PRO A 169 "
      ideal   model   delta    sigma   weight residual
     119.82  126.63   -6.81 9.80e-01 1.04e+00 4.83e+01
  angle pdb=" CA  ASP A 194 "
        pdb=" CB  ASP A 194 "
        pdb=" CG  ASP A 194 "
      ideal   model   delta    sigma   weight residual
     112.60  119.47   -6.87 1.00e+00 1.00e+00 4.72e+01
  angle pdb=" N   ILE A 757 "
        pdb=" CA  ILE A 757 "
        pdb=" C   ILE A 757 "
      ideal   model   delta    sigma   weight residual
     108.11  117.41   -9.30 1.40e+00 5.10e-01 4.41e+01
  ... (remaining 9205 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.22: 3896
       17.22 -    34.44: 103
       34.44 -    51.66: 16
       51.66 -    68.88: 9
       68.88 -    86.11: 5
  Dihedral angle restraints: 4029
    sinusoidal: 1576
      harmonic: 2453
  Sorted by residual:
  dihedral pdb=" C   HIS A 295 "
           pdb=" N   HIS A 295 "
           pdb=" CA  HIS A 295 "
           pdb=" CB  HIS A 295 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.98   -8.62     0      2.50e+00 1.60e-01 1.19e+01
  dihedral pdb=" N   ILE B 120 "
           pdb=" C   ILE B 120 "
           pdb=" CA  ILE B 120 "
           pdb=" CB  ILE B 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  131.72   -8.32     0      2.50e+00 1.60e-01 1.11e+01
  dihedral pdb=" CA  PRO A 830 "
           pdb=" C   PRO A 830 "
           pdb=" N   TYR A 831 "
           pdb=" CA  TYR A 831 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.43   16.57     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 4026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 623
       0.070 -    0.140: 281
       0.140 -    0.210: 89
       0.210 -    0.279: 29
       0.279 -    0.349: 4
  Chirality restraints: 1026
  Sorted by residual:
  chirality pdb=" CA  TYR A 867 "
            pdb=" N   TYR A 867 "
            pdb=" C   TYR A 867 "
            pdb=" CB  TYR A 867 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" CA  PHE B  92 "
            pdb=" N   PHE B  92 "
            pdb=" C   PHE B  92 "
            pdb=" CB  PHE B  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.03e+00
  chirality pdb=" CA  MET A 242 "
            pdb=" N   MET A 242 "
            pdb=" C   MET A 242 "
            pdb=" CB  MET A 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.38e+00
  ... (remaining 1023 not shown)

  Planarity restraints: 1176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 619 "    0.072 2.00e-02 2.50e+03   3.93e-02 3.09e+01
        pdb=" CG  TYR A 619 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 619 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 619 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 619 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 619 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 619 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 619 "    0.060 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 509 "   -0.046 2.00e-02 2.50e+03   2.25e-02 1.26e+01
        pdb=" CG  TRP A 509 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 509 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 509 "    0.027 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 509 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 509 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 509 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 509 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 509 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 509 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 237 "    0.048 2.00e-02 2.50e+03   2.50e-02 1.25e+01
        pdb=" CG  TYR A 237 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 237 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 237 "   -0.026 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 237 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 237 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 237 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 237 "    0.034 2.00e-02 2.50e+03
  ... (remaining 1173 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1997
        2.82 -     3.34: 6272
        3.34 -     3.86: 11632
        3.86 -     4.38: 14206
        4.38 -     4.90: 22527
  Nonbonded interactions: 56634
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 175 "
            pdb=" OH  TYR A 787 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OG1 THR A 189 "
            pdb=" OH  TYR A 237 "
     model   vdw
     2.418 3.040
  nonbonded pdb=" NZ  LYS A 478 "
            pdb=" OD1 ASP A 743 "
     model   vdw
     2.458 3.120
  nonbonded pdb=" N   ASP A 258 "
            pdb=" OD1 ASP A 258 "
     model   vdw
     2.460 3.120
  nonbonded pdb=" N   ASP B 112 "
            pdb=" OD1 ASP B 112 "
     model   vdw
     2.464 3.120
  ... (remaining 56629 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.030
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6704
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      :  0.019   0.721   6791  Z= 0.874
  Angle     :  1.646  25.451   9216  Z= 1.088
  Chirality :  0.090   0.349   1026
  Planarity :  0.009   0.039   1176
  Dihedral  :  9.782  86.106   2445
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 0.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.14 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.28), residues: 811
  helix: -0.34 (0.24), residues: 354
  sheet:  0.55 (0.60), residues: 63
  loop :  0.94 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 183 
 TYR   0.072   0.008   TYR A 619 
 PHE   0.032   0.006   PHE A 859 
 TRP   0.046   0.011   TRP A 509 
 HIS   0.017   0.002   HIS A 613 

Details of bonding type rmsd
  covalent geometry    : bond        0.01603 ( 6783)
  covalent geometry    : angle       1.56754 ( 9210)
  hydrogen bonds       : bond        0.16731 (  310)
  hydrogen bonds       : angle       6.70815 (  864)
  metal coordination   : bond        0.31958 (    8)
  metal coordination   : angle      19.78734 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 263
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 GLN cc_start: 0.7702 (mt0) cc_final: 0.7483 (mt0)
  outliers start: 1
  outliers final: 1
  residues processed: 264
  average time/residue: 0.0858
  time to fit residues: 29.5190
Evaluate side-chains
  168 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0020
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 572 HIS
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 ASN
A 752 HIS
A 769 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.195089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.172084 restraints weight = 8828.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.176934 restraints weight = 4121.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.179899 restraints weight = 2383.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.181654 restraints weight = 1595.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.182861 restraints weight = 1217.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.4106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6676
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6791  Z= 0.148
  Angle     :  0.617   6.622   9216  Z= 0.336
  Chirality :  0.044   0.227   1026
  Planarity :  0.005   0.045   1176
  Dihedral  :  4.822  36.603    909
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.66 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.29), residues: 811
  helix:  0.74 (0.27), residues: 360
  sheet:  0.36 (0.59), residues: 72
  loop :  0.58 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 733 
 TYR   0.023   0.002   TYR A 530 
 PHE   0.025   0.002   PHE A 471 
 TRP   0.021   0.002   TRP A 917 
 HIS   0.007   0.001   HIS A 872 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6783)
  covalent geometry    : angle       0.61435 ( 9210)
  hydrogen bonds       : bond        0.04930 (  310)
  hydrogen bonds       : angle       5.13246 (  864)
  metal coordination   : bond        0.01227 (    8)
  metal coordination   : angle       2.36059 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 168
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7674 (tttm) cc_final: 0.7123 (mmmt)
REVERT: A  173 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7613 (ptt90)
REVERT: A  509 TRP cc_start: 0.7376 (m-10) cc_final: 0.6862 (m-90)
REVERT: A  513 ARG cc_start: 0.6361 (ttm110) cc_final: 0.6161 (ttm110)
REVERT: A  657 ASN cc_start: 0.8013 (m-40) cc_final: 0.7756 (m110)
REVERT: A  666 MET cc_start: 0.5821 (mmm) cc_final: 0.4841 (mmm)
REVERT: A  913 THR cc_start: 0.7882 (m) cc_final: 0.7639 (t)
  outliers start: 15
  outliers final: 9
  residues processed: 174
  average time/residue: 0.0749
  time to fit residues: 17.5201
Evaluate side-chains
  152 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 142
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  483 TYR
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   chunk 64 optimal weight:    9.9990
   chunk 52 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0770
   overall best weight:    1.0142

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

Flipped N/Q/H residues before XYZ refinement:
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 ASN
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 ASN
B 168 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.186432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.163918 restraints weight = 8956.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.168407 restraints weight = 4251.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.171215 restraints weight = 2487.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.172859 restraints weight = 1686.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.174162 restraints weight = 1300.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6869
moved from start:          0.4196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6791  Z= 0.157
  Angle     :  0.568   6.510   9216  Z= 0.307
  Chirality :  0.043   0.150   1026
  Planarity :  0.004   0.043   1176
  Dihedral  :  4.744  31.069    909
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 12.07 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.29), residues: 811
  helix:  0.82 (0.27), residues: 359
  sheet:  0.30 (0.56), residues: 76
  loop :  0.39 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 111 
 TYR   0.022   0.002   TYR A 530 
 PHE   0.026   0.002   PHE A 753 
 TRP   0.011   0.001   TRP A 917 
 HIS   0.005   0.001   HIS A 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6783)
  covalent geometry    : angle       0.56606 ( 9210)
  hydrogen bonds       : bond        0.04005 (  310)
  hydrogen bonds       : angle       5.00701 (  864)
  metal coordination   : bond        0.00634 (    8)
  metal coordination   : angle       2.09886 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7479 (tttm) cc_final: 0.7053 (mmmt)
REVERT: A  173 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7810 (ptt90)
REVERT: A  324 THR cc_start: 0.8393 (p) cc_final: 0.8035 (t)
REVERT: A  343 SER cc_start: 0.8053 (m) cc_final: 0.7624 (m)
REVERT: A  509 TRP cc_start: 0.7501 (m-10) cc_final: 0.6911 (m-90)
REVERT: A  530 TYR cc_start: 0.8202 (t80) cc_final: 0.7997 (t80)
REVERT: A  657 ASN cc_start: 0.8158 (m-40) cc_final: 0.7451 (m110)
REVERT: A  666 MET cc_start: 0.5937 (mmm) cc_final: 0.4936 (mmm)
REVERT: A  668 MET cc_start: 0.8087 (mtp) cc_final: 0.7831 (mtp)
REVERT: A  714 LYS cc_start: 0.7706 (mmtm) cc_final: 0.6890 (tptp)
REVERT: A  794 MET cc_start: 0.6045 (ttp) cc_final: 0.5758 (ptm)
REVERT: B   87 MET cc_start: 0.8294 (mtm) cc_final: 0.8034 (mtm)
  outliers start: 20
  outliers final: 13
  residues processed: 165
  average time/residue: 0.0635
  time to fit residues: 14.6374
Evaluate side-chains
  159 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:    0.0970
   chunk 79 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 24 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0010
   chunk 81 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0000
   overall best weight:    0.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 790 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 = 0.4176 r_free = 0.4176 target = 0.189646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.167284 restraints weight = 8977.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.171914 restraints weight = 4245.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.174654 restraints weight = 2469.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.176586 restraints weight = 1678.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.177611 restraints weight = 1254.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6833
moved from start:          0.4552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6791  Z= 0.105
  Angle     :  0.499   5.536   9216  Z= 0.268
  Chirality :  0.040   0.129   1026
  Planarity :  0.004   0.042   1176
  Dihedral  :  4.428  23.181    907
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.85 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.30), residues: 811
  helix:  0.99 (0.28), residues: 361
  sheet:  0.42 (0.57), residues: 66
  loop :  0.35 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  96 
 TYR   0.016   0.001   TYR A 530 
 PHE   0.024   0.002   PHE A 753 
 TRP   0.015   0.001   TRP A 917 
 HIS   0.008   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 6783)
  covalent geometry    : angle       0.49700 ( 9210)
  hydrogen bonds       : bond        0.03482 (  310)
  hydrogen bonds       : angle       4.72654 (  864)
  metal coordination   : bond        0.00451 (    8)
  metal coordination   : angle       1.76635 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 158
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7585 (tttm) cc_final: 0.7140 (mmmt)
REVERT: A  167 GLU cc_start: 0.6596 (tm-30) cc_final: 0.6208 (tm-30)
REVERT: A  324 THR cc_start: 0.8383 (p) cc_final: 0.8068 (t)
REVERT: A  343 SER cc_start: 0.8012 (m) cc_final: 0.7565 (m)
REVERT: A  380 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.6431 (mtp)
REVERT: A  509 TRP cc_start: 0.7448 (m-10) cc_final: 0.6848 (m-90)
REVERT: A  540 THR cc_start: 0.7999 (t) cc_final: 0.7723 (t)
REVERT: A  657 ASN cc_start: 0.8181 (m-40) cc_final: 0.7454 (m110)
REVERT: A  666 MET cc_start: 0.5809 (mmm) cc_final: 0.4787 (mmm)
REVERT: A  714 LYS cc_start: 0.7695 (mmtm) cc_final: 0.6823 (tptp)
REVERT: A  794 MET cc_start: 0.6034 (ttp) cc_final: 0.5629 (ptm)
REVERT: B   87 MET cc_start: 0.8073 (mtm) cc_final: 0.7831 (mtm)
REVERT: B   88 GLN cc_start: 0.7247 (tp-100) cc_final: 0.6680 (tt0)
  outliers start: 15
  outliers final: 9
  residues processed: 164
  average time/residue: 0.0630
  time to fit residues: 14.4569
Evaluate side-chains
  147 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 137
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0570
   chunk 46 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.7098

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

Flipped N/Q/H residues before XYZ refinement:
** A 703 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 = 0.4121 r_free = 0.4121 target = 0.184256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.161066 restraints weight = 9009.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.165497 restraints weight = 4318.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.168298 restraints weight = 2549.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.170059 restraints weight = 1751.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.171101 restraints weight = 1341.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6899
moved from start:          0.4920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6791  Z= 0.124
  Angle     :  0.522   6.411   9216  Z= 0.277
  Chirality :  0.042   0.298   1026
  Planarity :  0.004   0.043   1176
  Dihedral  :  4.356  23.673    907
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.09 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.30), residues: 811
  helix:  0.98 (0.28), residues: 361
  sheet:  0.18 (0.54), residues: 81
  loop :  0.36 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  96 
 TYR   0.013   0.001   TYR A 619 
 PHE   0.030   0.002   PHE A 753 
 TRP   0.010   0.001   TRP A 917 
 HIS   0.006   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6783)
  covalent geometry    : angle       0.51987 ( 9210)
  hydrogen bonds       : bond        0.03455 (  310)
  hydrogen bonds       : angle       4.58503 (  864)
  metal coordination   : bond        0.00779 (    8)
  metal coordination   : angle       2.08629 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7616 (tttm) cc_final: 0.7146 (mmmt)
REVERT: A  167 GLU cc_start: 0.6571 (tm-30) cc_final: 0.6185 (tm-30)
REVERT: A  235 ASP cc_start: 0.6033 (m-30) cc_final: 0.5682 (t0)
REVERT: A  324 THR cc_start: 0.8410 (p) cc_final: 0.8080 (t)
REVERT: A  343 SER cc_start: 0.8084 (m) cc_final: 0.7643 (m)
REVERT: A  509 TRP cc_start: 0.7442 (m-10) cc_final: 0.6790 (m-90)
REVERT: A  540 THR cc_start: 0.8016 (t) cc_final: 0.7693 (t)
REVERT: A  653 TYR cc_start: 0.6701 (m-10) cc_final: 0.6483 (m-10)
REVERT: A  657 ASN cc_start: 0.8167 (m-40) cc_final: 0.7456 (m110)
REVERT: A  666 MET cc_start: 0.5759 (mmm) cc_final: 0.4812 (mmm)
REVERT: A  714 LYS cc_start: 0.7759 (mmtm) cc_final: 0.6875 (tptp)
REVERT: A  794 MET cc_start: 0.6157 (ttp) cc_final: 0.5685 (ptm)
  outliers start: 18
  outliers final: 14
  residues processed: 161
  average time/residue: 0.0591
  time to fit residues: 13.2343
Evaluate side-chains
  163 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 613 HIS
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 703 ASN
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.181394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.158153 restraints weight = 8949.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.162492 restraints weight = 4360.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.165245 restraints weight = 2613.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.166935 restraints weight = 1811.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.168042 restraints weight = 1399.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.5246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6791  Z= 0.132
  Angle     :  0.530   7.735   9216  Z= 0.279
  Chirality :  0.042   0.242   1026
  Planarity :  0.004   0.044   1176
  Dihedral  :  4.323  23.265    907
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 14.95 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.30), residues: 811
  helix:  0.95 (0.28), residues: 367
  sheet:  0.18 (0.56), residues: 81
  loop :  0.37 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  96 
 TYR   0.024   0.002   TYR A 530 
 PHE   0.021   0.002   PHE A 753 
 TRP   0.010   0.001   TRP A 917 
 HIS   0.005   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6783)
  covalent geometry    : angle       0.52685 ( 9210)
  hydrogen bonds       : bond        0.03503 (  310)
  hydrogen bonds       : angle       4.61475 (  864)
  metal coordination   : bond        0.00694 (    8)
  metal coordination   : angle       2.17311 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7696 (tttm) cc_final: 0.7221 (mmmt)
REVERT: A  167 GLU cc_start: 0.6709 (tm-30) cc_final: 0.6237 (tm-30)
REVERT: A  324 THR cc_start: 0.8350 (p) cc_final: 0.8074 (t)
REVERT: A  343 SER cc_start: 0.8167 (m) cc_final: 0.7740 (m)
REVERT: A  380 MET cc_start: 0.6885 (mmp) cc_final: 0.6548 (ttt)
REVERT: A  509 TRP cc_start: 0.7474 (m-90) cc_final: 0.6781 (m-90)
REVERT: A  540 THR cc_start: 0.8138 (t) cc_final: 0.7850 (t)
REVERT: A  657 ASN cc_start: 0.8276 (m-40) cc_final: 0.7603 (m110)
REVERT: A  666 MET cc_start: 0.5810 (mmm) cc_final: 0.4742 (mmm)
REVERT: A  714 LYS cc_start: 0.7729 (mmtm) cc_final: 0.6861 (tptp)
REVERT: A  794 MET cc_start: 0.6338 (ttp) cc_final: 0.5814 (ptm)
REVERT: A  825 ASP cc_start: 0.6886 (t70) cc_final: 0.6559 (p0)
  outliers start: 23
  outliers final: 18
  residues processed: 168
  average time/residue: 0.0636
  time to fit residues: 15.0217
Evaluate side-chains
  166 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 81 optimal weight:    7.9990
   chunk 79 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 HIS
A 657 ASN
A 661 GLN
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 118 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.169962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.147163 restraints weight = 9248.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.151079 restraints weight = 4598.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.153656 restraints weight = 2827.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.155164 restraints weight = 1997.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.156272 restraints weight = 1576.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.5883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   6791  Z= 0.288
  Angle     :  0.749  10.139   9216  Z= 0.393
  Chirality :  0.049   0.242   1026
  Planarity :  0.006   0.058   1176
  Dihedral  :  5.157  24.574    907
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 15.23 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.29), residues: 811
  helix:  0.40 (0.27), residues: 367
  sheet:  0.01 (0.55), residues: 83
  loop : -0.40 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 181 
 TYR   0.031   0.003   TYR A 530 
 PHE   0.036   0.003   PHE A 753 
 TRP   0.017   0.002   TRP B 182 
 HIS   0.008   0.002   HIS A 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00668 ( 6783)
  covalent geometry    : angle       0.74509 ( 9210)
  hydrogen bonds       : bond        0.04680 (  310)
  hydrogen bonds       : angle       5.25070 (  864)
  metal coordination   : bond        0.01897 (    8)
  metal coordination   : angle       3.03756 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 152
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7700 (tttm) cc_final: 0.7242 (mmmt)
REVERT: A  167 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6065 (tm-30)
REVERT: A  235 ASP cc_start: 0.6250 (m-30) cc_final: 0.5995 (t0)
REVERT: A  343 SER cc_start: 0.8281 (m) cc_final: 0.7863 (m)
REVERT: A  509 TRP cc_start: 0.7664 (m-90) cc_final: 0.7135 (m-90)
REVERT: A  540 THR cc_start: 0.8255 (t) cc_final: 0.8034 (t)
REVERT: A  653 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6741 (m-10)
REVERT: A  666 MET cc_start: 0.6190 (mmm) cc_final: 0.5210 (mmm)
REVERT: A  674 TYR cc_start: 0.7612 (m-80) cc_final: 0.7161 (m-80)
REVERT: A  714 LYS cc_start: 0.7943 (mmtm) cc_final: 0.6974 (tptp)
REVERT: A  825 ASP cc_start: 0.6873 (t70) cc_final: 0.6517 (p0)
  outliers start: 29
  outliers final: 21
  residues processed: 163
  average time/residue: 0.0601
  time to fit residues: 14.1733
Evaluate side-chains
  163 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  384 SER
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 29 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 118 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.177658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.154822 restraints weight = 9163.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.158968 restraints weight = 4427.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.161623 restraints weight = 2668.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.163203 restraints weight = 1855.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.163989 restraints weight = 1445.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.6005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6791  Z= 0.142
  Angle     :  0.619   8.473   9216  Z= 0.316
  Chirality :  0.043   0.203   1026
  Planarity :  0.004   0.049   1176
  Dihedral  :  4.810  23.454    907
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 16.46 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.29), residues: 811
  helix:  0.62 (0.28), residues: 370
  sheet:  0.05 (0.59), residues: 71
  loop : -0.26 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B  96 
 TYR   0.028   0.002   TYR A 530 
 PHE   0.054   0.002   PHE A 471 
 TRP   0.016   0.002   TRP A 917 
 HIS   0.004   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6783)
  covalent geometry    : angle       0.61766 ( 9210)
  hydrogen bonds       : bond        0.03587 (  310)
  hydrogen bonds       : angle       4.93471 (  864)
  metal coordination   : bond        0.00639 (    8)
  metal coordination   : angle       1.91069 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7815 (tttm) cc_final: 0.7336 (mmpt)
REVERT: A  167 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6229 (tm-30)
REVERT: A  235 ASP cc_start: 0.6186 (m-30) cc_final: 0.5913 (t0)
REVERT: A  343 SER cc_start: 0.8204 (m) cc_final: 0.7790 (m)
REVERT: A  372 LEU cc_start: 0.8549 (mt) cc_final: 0.8127 (tt)
REVERT: A  497 ASN cc_start: 0.8449 (t0) cc_final: 0.8008 (t0)
REVERT: A  509 TRP cc_start: 0.7568 (m-90) cc_final: 0.6950 (m-90)
REVERT: A  540 THR cc_start: 0.8273 (t) cc_final: 0.8064 (t)
REVERT: A  666 MET cc_start: 0.5930 (mmm) cc_final: 0.4871 (mmm)
REVERT: A  714 LYS cc_start: 0.7899 (mmtm) cc_final: 0.6994 (tptp)
REVERT: A  825 ASP cc_start: 0.6814 (t70) cc_final: 0.6457 (p0)
REVERT: B   96 ARG cc_start: 0.6679 (mmm160) cc_final: 0.6462 (mmm-85)
  outliers start: 20
  outliers final: 16
  residues processed: 158
  average time/residue: 0.0547
  time to fit residues: 12.6689
Evaluate side-chains
  157 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0670
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.179532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.156237 restraints weight = 9010.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.160422 restraints weight = 4374.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.163095 restraints weight = 2646.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.164692 restraints weight = 1842.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.165939 restraints weight = 1439.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7013
moved from start:          0.6155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6791  Z= 0.126
  Angle     :  0.578   7.975   9216  Z= 0.299
  Chirality :  0.042   0.182   1026
  Planarity :  0.004   0.045   1176
  Dihedral  :  4.622  23.083    907
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.28 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.30), residues: 811
  helix:  0.71 (0.28), residues: 372
  sheet: -0.05 (0.59), residues: 73
  loop : -0.17 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  96 
 TYR   0.024   0.001   TYR A 530 
 PHE   0.038   0.002   PHE A 471 
 TRP   0.023   0.002   TRP B 154 
 HIS   0.004   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6783)
  covalent geometry    : angle       0.57601 ( 9210)
  hydrogen bonds       : bond        0.03323 (  310)
  hydrogen bonds       : angle       4.80143 (  864)
  metal coordination   : bond        0.00529 (    8)
  metal coordination   : angle       1.85308 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7841 (tttm) cc_final: 0.7352 (mmpt)
REVERT: A  167 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6326 (tm-30)
REVERT: A  235 ASP cc_start: 0.6133 (m-30) cc_final: 0.5871 (t0)
REVERT: A  372 LEU cc_start: 0.8485 (mt) cc_final: 0.8034 (tt)
REVERT: A  380 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6394 (ttt)
REVERT: A  497 ASN cc_start: 0.8355 (t0) cc_final: 0.7979 (t0)
REVERT: A  509 TRP cc_start: 0.7478 (m-90) cc_final: 0.6856 (m-90)
REVERT: A  666 MET cc_start: 0.5676 (mmm) cc_final: 0.4684 (mmm)
REVERT: A  714 LYS cc_start: 0.7779 (mmtm) cc_final: 0.7067 (tptp)
REVERT: A  825 ASP cc_start: 0.6810 (t70) cc_final: 0.6451 (p0)
REVERT: B   96 ARG cc_start: 0.6653 (mmm160) cc_final: 0.6235 (mmm160)
  outliers start: 18
  outliers final: 16
  residues processed: 149
  average time/residue: 0.0580
  time to fit residues: 12.6037
Evaluate side-chains
  156 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 20 optimal weight:    0.3980
   chunk 72 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 76 optimal weight:    7.9990
   chunk 50 optimal weight:    0.0970
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 703 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.181514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.158214 restraints weight = 8984.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.162461 restraints weight = 4342.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.165101 restraints weight = 2613.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.166856 restraints weight = 1815.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.167865 restraints weight = 1398.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6984
moved from start:          0.6292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6791  Z= 0.111
  Angle     :  0.561   7.360   9216  Z= 0.287
  Chirality :  0.042   0.181   1026
  Planarity :  0.004   0.048   1176
  Dihedral  :  4.459  22.287    907
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 17.42 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.30), residues: 811
  helix:  0.86 (0.28), residues: 370
  sheet: -0.08 (0.57), residues: 79
  loop : -0.01 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  96 
 TYR   0.023   0.001   TYR A 530 
 PHE   0.033   0.002   PHE A 471 
 TRP   0.016   0.001   TRP B 154 
 HIS   0.004   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6783)
  covalent geometry    : angle       0.55946 ( 9210)
  hydrogen bonds       : bond        0.03099 (  310)
  hydrogen bonds       : angle       4.68693 (  864)
  metal coordination   : bond        0.00428 (    8)
  metal coordination   : angle       1.70034 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7844 (tttm) cc_final: 0.7388 (mmpt)
REVERT: A  167 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6359 (tm-30)
REVERT: A  235 ASP cc_start: 0.6242 (m-30) cc_final: 0.5981 (t0)
REVERT: A  343 SER cc_start: 0.8209 (m) cc_final: 0.7798 (m)
REVERT: A  380 MET cc_start: 0.6568 (mmp) cc_final: 0.6361 (ttt)
REVERT: A  497 ASN cc_start: 0.8341 (t0) cc_final: 0.8019 (t0)
REVERT: A  509 TRP cc_start: 0.7457 (m-90) cc_final: 0.6843 (m-90)
REVERT: A  666 MET cc_start: 0.5465 (mmm) cc_final: 0.4427 (mmm)
REVERT: A  714 LYS cc_start: 0.7784 (mmtm) cc_final: 0.7123 (tptp)
REVERT: A  825 ASP cc_start: 0.6797 (t70) cc_final: 0.6441 (p0)
REVERT: B   96 ARG cc_start: 0.6571 (mmm160) cc_final: 0.6133 (mmm160)
REVERT: B  149 TYR cc_start: 0.7411 (t80) cc_final: 0.6923 (t80)
  outliers start: 16
  outliers final: 15
  residues processed: 146
  average time/residue: 0.0674
  time to fit residues: 14.1076
Evaluate side-chains
  148 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  208 ASP
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 70 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 12 optimal weight:    0.1980
   chunk 66 optimal weight:    0.0670
   chunk 42 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 703 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.182584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.160092 restraints weight = 8881.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.164310 restraints weight = 4284.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.166791 restraints weight = 2571.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.168610 restraints weight = 1797.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.169805 restraints weight = 1368.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
moved from start:          0.6363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6791  Z= 0.109
  Angle     :  0.554   7.632   9216  Z= 0.284
  Chirality :  0.042   0.212   1026
  Planarity :  0.004   0.052   1176
  Dihedral  :  4.382  21.998    907
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 17.56 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.31), residues: 811
  helix:  0.93 (0.28), residues: 369
  sheet:  0.01 (0.57), residues: 79
  loop :  0.10 (0.35), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  96 
 TYR   0.022   0.001   TYR A 530 
 PHE   0.030   0.002   PHE A 471 
 TRP   0.018   0.002   TRP B 154 
 HIS   0.004   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6783)
  covalent geometry    : angle       0.55257 ( 9210)
  hydrogen bonds       : bond        0.03091 (  310)
  hydrogen bonds       : angle       4.65459 (  864)
  metal coordination   : bond        0.00405 (    8)
  metal coordination   : angle       1.64675 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1115.44 seconds
wall clock time: 19 minutes 56.67 seconds (1196.67 seconds total)