Starting phenix.real_space_refine
on Sat Jul 26 10:48:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bw4_30226/07_2025/7bw4_30226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bw4_30226/07_2025/7bw4_30226.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bw4_30226/07_2025/7bw4_30226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bw4_30226/07_2025/7bw4_30226.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bw4_30226/07_2025/7bw4_30226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bw4_30226/07_2025/7bw4_30226.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.002
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      63      5.16       5
     C    5503      2.51       5
     N    1430      2.21       5
     O    1607      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8605
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 811, 6541
          Classifications: {'peptide': 811}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 783}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 890
          Classifications: {'peptide': 115}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109}
    Chain: "C"
      Number of atoms: 496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 496
          Classifications: {'peptide': 65}
          Link IDs: {'TRANS': 64}
    Chain: "D"
      Number of atoms: 676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 676
          Classifications: {'peptide': 87}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 82}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    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   1681  SG  CYS A 301      37.606  64.202  36.311  1.00 60.22           S
  ATOM   1722  SG  CYS A 306      37.746  61.966  32.323  1.00 54.47           S
  ATOM   1754  SG  CYS A 310      40.444  62.538  35.190  1.00 51.56           S
  ATOM   3162  SG  CYS A 487      18.959  60.096  44.561  1.00 74.40           S
  ATOM   4415  SG  CYS A 645      18.857  59.240  41.138  1.00 73.86           S
  ATOM   4421  SG  CYS A 646      21.336  61.568  42.144  1.00 71.79           S

  Time building chain proxies: 5.44, per 1000 atoms: 0.63
  Number of scatterers: 8605
  At special positions: 0
  Unit cell: (80.8, 95.2, 124, 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      63     16.00
     O    1607      8.00
     N    1430      7.00
     C    5503      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: 2.27
  Conformation dependent library (CDL) restraints added in 969.3 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 306 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 310 "
        pdb="ZN    ZN A1001 " - pdb=" ND1 HIS A 295 "
      pdb="  ZN A1002 "
        pdb="ZN    ZN A1002 " - pdb=" ND1 HIS A 642 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 487 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 646 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 645 "
      Number of angles added : 6


  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2066

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 10 sheets defined
      51.5% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 133
    Processing helix  chain 'A' and resid 139 through 149
      removed outlier: 4.058A  pdb=" N   TYR A 149 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 159
      removed outlier: 3.611A  pdb=" N   PHE A 157 " --> pdb=" O   ASP A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 187
      removed outlier: 3.590A  pdb=" N   TYR A 175 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASN A 177 " --> pdb=" O   ARG A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 197
      removed outlier: 3.628A  pdb=" N   CYS A 193 " --> pdb=" O   THR A 189 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ASP A 194 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ALA A 195 " --> pdb=" O   GLN A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 210
      removed outlier: 3.781A  pdb=" N   ASN A 209 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 242
      removed outlier: 3.615A  pdb=" N   TYR A 238 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 246
      removed outlier: 4.200A  pdb=" N   THR A 246 " --> pdb=" O   PRO A 243 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 243 through 246'
    Processing helix  chain 'A' and resid 250 through 255
    Processing helix  chain 'A' and resid 275 through 287
    Processing helix  chain 'A' and resid 297 through 301
      removed outlier: 3.710A  pdb=" N   ASN A 300 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   CYS A 301 " --> pdb=" O   CYS A 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 297 through 301'
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 367 through 377
    Processing helix  chain 'A' and resid 378 through 384
    Processing helix  chain 'A' and resid 416 through 426
      removed outlier: 3.938A  pdb=" N   TYR A 420 " --> pdb=" O   ASN A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 458
    Processing helix  chain 'A' and resid 466 through 480
    Processing helix  chain 'A' and resid 511 through 519
      removed outlier: 3.735A  pdb=" N   TYR A 515 " --> pdb=" O   LYS A 511 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   MET A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 532
    Processing helix  chain 'A' and resid 561 through 581
      removed outlier: 3.649A  pdb=" N   THR A 565 " --> pdb=" O   SER A 561 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA A 581 " --> pdb=" O   LYS A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 607
    Processing helix  chain 'A' and resid 621 through 626
    Processing helix  chain 'A' and resid 627 through 641
      removed outlier: 3.728A  pdb=" N   ARG A 631 " --> pdb=" O   PRO A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 663
    Processing helix  chain 'A' and resid 684 through 709
      removed outlier: 4.208A  pdb=" N   ALA A 688 " --> pdb=" O   ASP A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 733
    Processing helix  chain 'A' and resid 738 through 752
    Processing helix  chain 'A' and resid 768 through 774
    Processing helix  chain 'A' and resid 778 through 791
      removed outlier: 3.952A  pdb=" N   PHE A 782 " --> pdb=" O   SER A 778 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASN A 791 " --> pdb=" O   TYR A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 799
      removed outlier: 3.571A  pdb=" N   CYS A 799 " --> pdb=" O   GLU A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 842
      removed outlier: 3.648A  pdb=" N   ILE A 837 " --> pdb=" O   ASP A 833 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 851 through 866
      removed outlier: 4.046A  pdb=" N   MET A 855 " --> pdb=" O   ASP A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 872
    Processing helix  chain 'A' and resid 874 through 895
      removed outlier: 4.166A  pdb=" N   ALA A 878 " --> pdb=" O   ASN A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 918 through 923
    Processing helix  chain 'A' and resid 924 through 926
      No H-bonds generated for 'chain 'A' and resid 924 through 926'
    Processing helix  chain 'B' and resid 79 through 97
      removed outlier: 3.648A  pdb=" N   LYS B  97 " --> pdb=" O   THR B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 109
    Processing helix  chain 'B' and resid 119 through 124
    Processing helix  chain 'B' and resid 134 through 142
      removed outlier: 3.608A  pdb=" N   TYR B 138 " --> pdb=" O   ASP B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 172
      removed outlier: 3.601A  pdb=" N   ILE B 172 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 180
    Processing helix  chain 'C' and resid 3 through 20
      removed outlier: 4.020A  pdb=" N   LYS C   7 " --> pdb=" O   MET C   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 24
      removed outlier: 3.563A  pdb=" N   SER C  24 " --> pdb=" O   ARG C  21 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 21 through 24'
    Processing helix  chain 'C' and resid 25 through 40
    Processing helix  chain 'C' and resid 46 through 62
      removed outlier: 3.649A  pdb=" N   GLU C  50 " --> pdb=" O   THR C  46 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   MET C  62 " --> pdb=" O   VAL C  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 99
      removed outlier: 3.775A  pdb=" N   ASP D  99 " --> pdb=" O   LEU D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 113
      removed outlier: 3.576A  pdb=" N   ASN D 104 " --> pdb=" O   ASN D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 134 through 141
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38
      removed outlier: 4.178A  pdb=" N   ILE A  37 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY A  44 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224
      removed outlier: 5.836A  pdb=" N   ILE A 201 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   VAL A 233 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   GLY A 203 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 355
      removed outlier: 6.320A  pdb=" N   LEU A 329 " --> pdb=" O   THR A 344 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   TYR A 346 " --> pdb=" O   GLY A 327 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   GLY A 327 " --> pdb=" O   TYR A 346 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 390
      removed outlier: 3.567A  pdb=" N   VAL B 131 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   THR B 187 " --> pdb=" O   GLN B 158 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   GLN B 158 " --> pdb=" O   THR B 187 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   LEU B 189 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   ILE B 156 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   ALA B 191 " --> pdb=" O   TRP B 154 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   TRP B 154 " --> pdb=" O   ALA B 191 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 414 through 415
    Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559
      removed outlier: 6.427A  pdb=" N   THR A 540 " --> pdb=" O   MET A 668 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758
    Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 821
    Processing sheet with id=AA9, first strand: chain 'D' and resid 115 through 116
      removed outlier: 4.120A  pdb=" N   VAL D 115 " --> pdb=" O   VAL D 131 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA D 188 " --> pdb=" O   LEU D 128 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   VAL D 130 " --> pdb=" O   VAL D 186 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL D 186 " --> pdb=" O   VAL D 130 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   LEU D 189 " --> pdb=" O   GLU D 155 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   GLU D 155 " --> pdb=" O   LEU D 189 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 142 through 143

    396 hydrogen bonds defined for protein.
    1131 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: 2.62

  Time building geometry restraints manager: 2.68 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2411
        1.33 -     1.45: 1541
        1.45 -     1.57: 4746
        1.57 -     1.69: 0
        1.69 -     1.81: 96
  Bond restraints: 8794
  Sorted by residual:
  bond pdb=" N   LEU A 401 "
       pdb=" CA  LEU A 401 "
    ideal  model  delta    sigma   weight residual
    1.458  1.499 -0.041 1.37e-02 5.33e+03 8.89e+00
  bond pdb=" N   THR A 248 "
       pdb=" CA  THR A 248 "
    ideal  model  delta    sigma   weight residual
    1.455  1.495 -0.041 1.37e-02 5.33e+03 8.86e+00
  bond pdb=" N   ARG A 249 "
       pdb=" CA  ARG A 249 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.037 1.29e-02 6.01e+03 8.36e+00
  bond pdb=" N   VAL A 166 "
       pdb=" CA  VAL A 166 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.18e+00
  bond pdb=" N   VAL A 174 "
       pdb=" CA  VAL A 174 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.84e+00
  ... (remaining 8789 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 11592
        1.73 -     3.46: 293
        3.46 -     5.19: 48
        5.19 -     6.92: 3
        6.92 -     8.65: 2
  Bond angle restraints: 11938
  Sorted by residual:
  angle pdb=" C   THR A 248 "
        pdb=" CA  THR A 248 "
        pdb=" CB  THR A 248 "
      ideal   model   delta    sigma   weight residual
     109.55  116.90   -7.35 1.68e+00 3.54e-01 1.91e+01
  angle pdb=" C   VAL A 166 "
        pdb=" CA  VAL A 166 "
        pdb=" CB  VAL A 166 "
      ideal   model   delta    sigma   weight residual
     111.29  104.38    6.91 1.64e+00 3.72e-01 1.78e+01
  angle pdb=" N   VAL A 166 "
        pdb=" CA  VAL A 166 "
        pdb=" C   VAL A 166 "
      ideal   model   delta    sigma   weight residual
     109.34  117.99   -8.65 2.08e+00 2.31e-01 1.73e+01
  angle pdb=" N   ASN A 447 "
        pdb=" CA  ASN A 447 "
        pdb=" C   ASN A 447 "
      ideal   model   delta    sigma   weight residual
     111.71  106.96    4.75 1.15e+00 7.56e-01 1.71e+01
  angle pdb=" N   LEU A 247 "
        pdb=" CA  LEU A 247 "
        pdb=" C   LEU A 247 "
      ideal   model   delta    sigma   weight residual
     111.82  107.38    4.44 1.16e+00 7.43e-01 1.47e+01
  ... (remaining 11933 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 4637
       17.99 -    35.98: 495
       35.98 -    53.97: 78
       53.97 -    71.95: 12
       71.95 -    89.94: 8
  Dihedral angle restraints: 5230
    sinusoidal: 2035
      harmonic: 3195
  Sorted by residual:
  dihedral pdb=" CA  ASP D 161 "
           pdb=" C   ASP D 161 "
           pdb=" N   ALA D 162 "
           pdb=" CA  ALA D 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.73   29.27     0      5.00e+00 4.00e-02 3.43e+01
  dihedral pdb=" CA  THR A 462 "
           pdb=" C   THR A 462 "
           pdb=" N   MET A 463 "
           pdb=" CA  MET A 463 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.65   27.35     0      5.00e+00 4.00e-02 2.99e+01
  dihedral pdb=" CA  TRP A 617 "
           pdb=" C   TRP A 617 "
           pdb=" N   ASP A 618 "
           pdb=" CA  ASP A 618 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.05   26.95     0      5.00e+00 4.00e-02 2.91e+01
  ... (remaining 5227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 988
       0.055 -    0.111: 295
       0.111 -    0.166: 53
       0.166 -    0.221: 11
       0.221 -    0.276: 3
  Chirality restraints: 1350
  Sorted by residual:
  chirality pdb=" CA  LEU A 251 "
            pdb=" N   LEU A 251 "
            pdb=" C   LEU A 251 "
            pdb=" CB  LEU A 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" CA  THR A 248 "
            pdb=" N   THR A 248 "
            pdb=" C   THR A 248 "
            pdb=" CB  THR A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CA  SER B 177 "
            pdb=" N   SER B 177 "
            pdb=" C   SER B 177 "
            pdb=" CB  SER B 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.49e+00
  ... (remaining 1347 not shown)

  Planarity restraints: 1517
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 686 "   -0.018 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   THR A 686 "    0.063 2.00e-02 2.50e+03
        pdb=" O   THR A 686 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   THR A 687 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 572 "   -0.016 2.00e-02 2.50e+03   3.28e-02 1.08e+01
        pdb=" C   HIS A 572 "    0.057 2.00e-02 2.50e+03
        pdb=" O   HIS A 572 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLN A 573 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 570 "   -0.016 2.00e-02 2.50e+03   3.22e-02 1.04e+01
        pdb=" C   GLN A 570 "    0.056 2.00e-02 2.50e+03
        pdb=" O   GLN A 570 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   PHE A 571 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1514 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 148
        2.64 -     3.21: 8024
        3.21 -     3.77: 13095
        3.77 -     4.34: 17510
        4.34 -     4.90: 28137
  Nonbonded interactions: 66914
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 168 "
            pdb=" ND2 ASN A 168 "
     model   vdw
     2.078 3.120
  nonbonded pdb=" N   LYS D 127 "
            pdb=" O   ALA D 188 "
     model   vdw
     2.159 3.120
  nonbonded pdb=" OG1 THR A 120 "
            pdb=" O   TYR A 122 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OH  TYR A 122 "
            pdb=" OE1 GLU A 144 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   VAL A 174 "
            pdb=" N   ASN A 177 "
     model   vdw
     2.193 3.120
  ... (remaining 66909 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:             1.510
  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:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.260
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
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      :  0.007   0.472   8802  Z= 0.279
  Angle     :  0.791  32.606  11944  Z= 0.436
  Chirality :  0.055   0.276   1350
  Planarity :  0.004   0.042   1517
  Dihedral  : 15.164  89.943   3164
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.34 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  4.73 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.22), residues: 1060
  helix: -0.74 (0.21), residues: 493
  sheet: -1.63 (0.55), residues: 76
  loop : -2.66 (0.22), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 154 
 HIS   0.004   0.001   HIS A 309 
 PHE   0.017   0.001   PHE A 571 
 TYR   0.013   0.001   TYR A 453 
 ARG   0.002   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15721 (  396)
  hydrogen bonds       : angle       6.09662 ( 1131)
  metal coordination   : bond        0.19302 (    8)
  metal coordination   : angle      19.77167 (    6)
  covalent geometry    : bond        0.00372 ( 8794)
  covalent geometry    : angle       0.65530 (11938)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 256
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7484 (m-80) cc_final: 0.7121 (m-80)
REVERT: A  191 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7216 (tm-30)
REVERT: A  217 TYR cc_start: 0.6078 (p90) cc_final: 0.5854 (p90)
REVERT: A  316 LEU cc_start: 0.7504 (tp) cc_final: 0.7298 (tt)
REVERT: A  500 LYS cc_start: 0.6395 (mttp) cc_final: 0.5666 (tttm)
REVERT: A  548 ILE cc_start: 0.8426 (mp) cc_final: 0.8121 (mp)
REVERT: A  575 LEU cc_start: 0.7481 (tp) cc_final: 0.7233 (tt)
REVERT: A  868 PRO cc_start: 0.8302 (Cg_exo) cc_final: 0.8011 (Cg_endo)
REVERT: A  882 HIS cc_start: 0.8059 (m-70) cc_final: 0.7858 (m90)
REVERT: A  889 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7325 (mmt90)
REVERT: B   91 LEU cc_start: 0.9249 (mt) cc_final: 0.8839 (mt)
REVERT: C   18 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7730 (tm-30)
REVERT: C   31 GLN cc_start: 0.7389 (mt0) cc_final: 0.7078 (mt0)
REVERT: C   51 LYS cc_start: 0.8731 (mttm) cc_final: 0.8482 (mmtp)
  outliers start: 16
  outliers final: 7
  residues processed: 268
  average time/residue: 0.2614
  time to fit residues: 90.9771
Evaluate side-chains
  192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 184
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  191 GLN
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  196 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 83 optimal weight:    9.9990
   chunk 32 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 96 optimal weight:    0.0970
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
A 191 GLN
A 210 GLN
A 213 ASN
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 386 ASN
A 439 HIS
A 447 ASN
A 497 ASN
A 568 ASN
A 572 HIS
A 650 HIS
A 703 ASN
A 713 ASN
A 722 ASN
A 789 GLN
A 928 HIS
B 104 ASN
B 118 ASN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 104 ASN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.140501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.114324 restraints weight = 16840.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.117675 restraints weight = 9409.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.119906 restraints weight = 6397.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8802  Z= 0.149
  Angle     :  0.646   9.442  11944  Z= 0.345
  Chirality :  0.046   0.193   1350
  Planarity :  0.004   0.044   1517
  Dihedral  :  6.782  89.082   1187
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.77 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.46 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.24), residues: 1060
  helix: -0.01 (0.23), residues: 508
  sheet: -1.71 (0.57), residues: 66
  loop : -2.16 (0.24), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 617 
 HIS   0.005   0.001   HIS A 309 
 PHE   0.012   0.001   PHE B 147 
 TYR   0.018   0.001   TYR A 887 
 ARG   0.006   0.001   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05385 (  396)
  hydrogen bonds       : angle       5.30715 ( 1131)
  metal coordination   : bond        0.00981 (    8)
  metal coordination   : angle       2.98986 (    6)
  covalent geometry    : bond        0.00314 ( 8794)
  covalent geometry    : angle       0.64310 (11938)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 200
  time to evaluate  : 1.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7285 (m-80) cc_final: 0.6731 (m-80)
REVERT: A  316 LEU cc_start: 0.7790 (tp) cc_final: 0.7533 (tt)
REVERT: A  456 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7029 (t80)
REVERT: A  500 LYS cc_start: 0.6060 (mttp) cc_final: 0.5736 (tttm)
REVERT: A  889 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7396 (mmt90)
REVERT: C   21 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8268 (mtm-85)
REVERT: C   31 GLN cc_start: 0.7249 (mt0) cc_final: 0.6985 (mt0)
REVERT: D   87 MET cc_start: 0.6453 (tpt) cc_final: 0.6240 (tpt)
  outliers start: 22
  outliers final: 12
  residues processed: 212
  average time/residue: 0.2108
  time to fit residues: 61.7414
Evaluate side-chains
  188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 174
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  196 MET
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  818 MET
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   21 ARG
Chi-restraints excluded: chain C residue   45 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 78 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 86 optimal weight:    5.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
A 191 GLN
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 HIS
A 599 HIS
A 882 HIS
B 158 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.135422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.108367 restraints weight = 17190.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.111500 restraints weight = 9741.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.113701 restraints weight = 6746.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8802  Z= 0.189
  Angle     :  0.658   8.924  11944  Z= 0.356
  Chirality :  0.046   0.244   1350
  Planarity :  0.004   0.042   1517
  Dihedral  :  5.613  52.604   1177
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.43 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 15.88 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.24), residues: 1060
  helix:  0.27 (0.23), residues: 505
  sheet: -1.75 (0.51), residues: 79
  loop : -2.00 (0.25), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 154 
 HIS   0.015   0.001   HIS A 882 
 PHE   0.015   0.002   PHE A 766 
 TYR   0.022   0.002   TYR A 453 
 ARG   0.006   0.000   ARG A 836 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05928 (  396)
  hydrogen bonds       : angle       5.47446 ( 1131)
  metal coordination   : bond        0.01813 (    8)
  metal coordination   : angle       2.34339 (    6)
  covalent geometry    : bond        0.00419 ( 8794)
  covalent geometry    : angle       0.65613 (11938)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 182
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A   35 PHE cc_start: 0.7289 (m-80) cc_final: 0.6729 (m-80)
REVERT: A  456 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7013 (t80)
REVERT: A  500 LYS cc_start: 0.6311 (mttp) cc_final: 0.5836 (tttm)
REVERT: A  575 LEU cc_start: 0.7879 (tp) cc_final: 0.7531 (tt)
REVERT: A  889 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7472 (mmt90)
REVERT: B   90 MET cc_start: 0.8242 (tmm) cc_final: 0.7884 (tmm)
REVERT: C   31 GLN cc_start: 0.7527 (mt0) cc_final: 0.7203 (mt0)
REVERT: D  129 MET cc_start: 0.7296 (tpp) cc_final: 0.7072 (tpt)
  outliers start: 36
  outliers final: 21
  residues processed: 204
  average time/residue: 0.2209
  time to fit residues: 61.5587
Evaluate side-chains
  183 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 1.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  468 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  804 ASP
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  184 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 102 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 81 optimal weight:    0.2980
   chunk 72 optimal weight:    7.9990
   chunk 67 optimal weight:    0.6980
   chunk 104 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   chunk 105 optimal weight:    6.9990
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.134880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.108181 restraints weight = 17093.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.111345 restraints weight = 9676.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.113499 restraints weight = 6663.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8802  Z= 0.191
  Angle     :  0.650   8.806  11944  Z= 0.351
  Chirality :  0.046   0.166   1350
  Planarity :  0.004   0.050   1517
  Dihedral  :  5.405  54.309   1174
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 16.93 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.24), residues: 1060
  helix:  0.26 (0.23), residues: 508
  sheet: -1.58 (0.44), residues: 99
  loop : -2.00 (0.26), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 154 
 HIS   0.003   0.001   HIS A 309 
 PHE   0.016   0.002   PHE B 147 
 TYR   0.029   0.002   TYR A 453 
 ARG   0.005   0.001   ARG A 836 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05886 (  396)
  hydrogen bonds       : angle       5.51499 ( 1131)
  metal coordination   : bond        0.01925 (    8)
  metal coordination   : angle       1.95060 (    6)
  covalent geometry    : bond        0.00423 ( 8794)
  covalent geometry    : angle       0.64874 (11938)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 177
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7278 (m-80) cc_final: 0.6790 (m-80)
REVERT: A  346 TYR cc_start: 0.7938 (t80) cc_final: 0.7730 (t80)
REVERT: A  456 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7136 (t80)
REVERT: A  822 GLN cc_start: 0.7825 (tm-30) cc_final: 0.6925 (tm-30)
REVERT: A  825 ASP cc_start: 0.7053 (p0) cc_final: 0.6136 (p0)
REVERT: A  889 ARG cc_start: 0.8124 (mtt90) cc_final: 0.7421 (mmt90)
REVERT: C   27 LYS cc_start: 0.6478 (OUTLIER) cc_final: 0.6189 (pttt)
REVERT: C   31 GLN cc_start: 0.7593 (mt0) cc_final: 0.7265 (mt0)
REVERT: C   38 ASP cc_start: 0.7716 (t0) cc_final: 0.7474 (t0)
REVERT: D  139 LYS cc_start: 0.8302 (mmtt) cc_final: 0.8073 (ptpt)
  outliers start: 42
  outliers final: 26
  residues processed: 205
  average time/residue: 0.2883
  time to fit residues: 82.2260
Evaluate side-chains
  190 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 162
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  468 GLN
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  737 VAL
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  804 ASP
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  845 ASP
Chi-restraints excluded: chain A residue  926 THR
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   27 LYS
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  189 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 88 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 789 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.132309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.105678 restraints weight = 17171.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.108742 restraints weight = 9906.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.110821 restraints weight = 6873.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.3448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   8802  Z= 0.228
  Angle     :  0.696   8.741  11944  Z= 0.374
  Chirality :  0.047   0.177   1350
  Planarity :  0.004   0.053   1517
  Dihedral  :  5.534  53.946   1174
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.75 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 19.56 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.24), residues: 1060
  helix:  0.21 (0.23), residues: 507
  sheet: -1.35 (0.54), residues: 74
  loop : -2.00 (0.25), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 154 
 HIS   0.004   0.001   HIS A 642 
 PHE   0.017   0.002   PHE A 766 
 TYR   0.034   0.002   TYR A 453 
 ARG   0.004   0.001   ARG B 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06366 (  396)
  hydrogen bonds       : angle       5.65392 ( 1131)
  metal coordination   : bond        0.02287 (    8)
  metal coordination   : angle       2.17717 (    6)
  covalent geometry    : bond        0.00513 ( 8794)
  covalent geometry    : angle       0.69417 (11938)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 177
  time to evaluate  : 1.064 
Fit side-chains
REVERT: A   35 PHE cc_start: 0.7366 (m-80) cc_final: 0.6913 (m-80)
REVERT: A  456 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.6985 (t80)
REVERT: A  822 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7061 (tm-30)
REVERT: A  825 ASP cc_start: 0.7113 (p0) cc_final: 0.6358 (p0)
REVERT: A  889 ARG cc_start: 0.8137 (mtt90) cc_final: 0.7450 (mtt-85)
REVERT: C   27 LYS cc_start: 0.6646 (OUTLIER) cc_final: 0.6346 (pttt)
REVERT: C   31 GLN cc_start: 0.7580 (mt0) cc_final: 0.7224 (mt0)
REVERT: D  129 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6730 (tpt)
REVERT: D  139 LYS cc_start: 0.8316 (mmtt) cc_final: 0.8082 (ptpt)
  outliers start: 45
  outliers final: 32
  residues processed: 205
  average time/residue: 0.2418
  time to fit residues: 68.2052
Evaluate side-chains
  202 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 167
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  468 GLN
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  737 VAL
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  804 ASP
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  845 ASP
Chi-restraints excluded: chain A residue  926 THR
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   27 LYS
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  129 MET
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  167 VAL
Chi-restraints excluded: chain D residue  189 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 104 optimal weight:    8.9990
   chunk 103 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 58 optimal weight:    8.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 381 HIS
** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.136152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.109674 restraints weight = 16916.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.112921 restraints weight = 9711.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.115076 restraints weight = 6677.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8802  Z= 0.155
  Angle     :  0.634   9.941  11944  Z= 0.338
  Chirality :  0.045   0.177   1350
  Planarity :  0.004   0.046   1517
  Dihedral  :  5.357  57.130   1174
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 21.35 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.25), residues: 1060
  helix:  0.34 (0.23), residues: 510
  sheet: -1.29 (0.55), residues: 74
  loop : -1.83 (0.25), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 154 
 HIS   0.004   0.001   HIS A 309 
 PHE   0.013   0.001   PHE A 287 
 TYR   0.028   0.001   TYR A 453 
 ARG   0.004   0.000   ARG B  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05352 (  396)
  hydrogen bonds       : angle       5.43400 ( 1131)
  metal coordination   : bond        0.01180 (    8)
  metal coordination   : angle       1.61401 (    6)
  covalent geometry    : bond        0.00338 ( 8794)
  covalent geometry    : angle       0.63310 (11938)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 191
  time to evaluate  : 1.543 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7318 (m-80) cc_final: 0.6804 (m-80)
REVERT: A  217 TYR cc_start: 0.5805 (p90) cc_final: 0.5127 (p90)
REVERT: A  456 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7130 (t80)
REVERT: A  668 MET cc_start: 0.7434 (tpt) cc_final: 0.7111 (tpt)
REVERT: A  822 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7028 (tm-30)
REVERT: A  825 ASP cc_start: 0.7077 (p0) cc_final: 0.6417 (p0)
REVERT: A  889 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7371 (mtt-85)
REVERT: C   27 LYS cc_start: 0.6456 (OUTLIER) cc_final: 0.6188 (pttt)
REVERT: C   31 GLN cc_start: 0.7662 (mt0) cc_final: 0.7228 (mt0)
REVERT: D  108 ASN cc_start: 0.8194 (m-40) cc_final: 0.7972 (m110)
REVERT: D  139 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8096 (ptpt)
  outliers start: 39
  outliers final: 29
  residues processed: 214
  average time/residue: 0.2382
  time to fit residues: 69.5873
Evaluate side-chains
  207 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 176
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  468 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  542 MET
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  804 ASP
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue   27 LYS
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  165 LYS
Chi-restraints excluded: chain D residue  189 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 88 optimal weight:    0.1980
   chunk 80 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 72 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 789 GLN
A 810 HIS
C  19 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.138273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.112147 restraints weight = 17080.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.115486 restraints weight = 9688.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.117645 restraints weight = 6635.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8802  Z= 0.141
  Angle     :  0.626   9.359  11944  Z= 0.334
  Chirality :  0.045   0.193   1350
  Planarity :  0.004   0.047   1517
  Dihedral  :  5.212  58.360   1174
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 22.08 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.25), residues: 1060
  helix:  0.53 (0.23), residues: 505
  sheet: -1.34 (0.51), residues: 84
  loop : -1.73 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 154 
 HIS   0.004   0.001   HIS A 309 
 PHE   0.016   0.001   PHE A 340 
 TYR   0.024   0.001   TYR A 453 
 ARG   0.004   0.000   ARG A 640 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05139 (  396)
  hydrogen bonds       : angle       5.35365 ( 1131)
  metal coordination   : bond        0.00883 (    8)
  metal coordination   : angle       1.33024 (    6)
  covalent geometry    : bond        0.00304 ( 8794)
  covalent geometry    : angle       0.62529 (11938)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 190
  time to evaluate  : 1.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7374 (m-80) cc_final: 0.6844 (m-80)
REVERT: A  217 TYR cc_start: 0.5795 (p90) cc_final: 0.5182 (p90)
REVERT: A  456 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7144 (t80)
REVERT: A  575 LEU cc_start: 0.7349 (tp) cc_final: 0.6445 (tt)
REVERT: A  759 SER cc_start: 0.8733 (p) cc_final: 0.8508 (m)
REVERT: A  822 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7034 (tm-30)
REVERT: A  889 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7301 (mmt90)
REVERT: B   82 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8764 (tptt)
REVERT: C   27 LYS cc_start: 0.6295 (OUTLIER) cc_final: 0.6075 (pttt)
REVERT: C   31 GLN cc_start: 0.7605 (mt0) cc_final: 0.7179 (mt0)
REVERT: D   92 PHE cc_start: 0.8401 (m-80) cc_final: 0.8186 (m-80)
REVERT: D  139 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8098 (ptpt)
  outliers start: 41
  outliers final: 33
  residues processed: 217
  average time/residue: 0.2966
  time to fit residues: 90.4789
Evaluate side-chains
  210 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 175
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  468 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  542 MET
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  788 TYR
Chi-restraints excluded: chain A residue  804 ASP
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   27 LYS
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  165 LYS
Chi-restraints excluded: chain D residue  167 VAL
Chi-restraints excluded: chain D residue  189 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 96 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   chunk 104 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.137022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.110531 restraints weight = 17344.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.113799 restraints weight = 9855.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.115972 restraints weight = 6737.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.3985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8802  Z= 0.155
  Angle     :  0.671  10.821  11944  Z= 0.352
  Chirality :  0.046   0.200   1350
  Planarity :  0.004   0.046   1517
  Dihedral  :  5.266  58.268   1174
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 23.55 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.25), residues: 1060
  helix:  0.52 (0.23), residues: 508
  sheet: -0.99 (0.49), residues: 94
  loop : -1.82 (0.26), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 154 
 HIS   0.005   0.001   HIS A 309 
 PHE   0.022   0.001   PHE A 287 
 TYR   0.023   0.001   TYR A 453 
 ARG   0.004   0.000   ARG B 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05352 (  396)
  hydrogen bonds       : angle       5.40094 ( 1131)
  metal coordination   : bond        0.01286 (    8)
  metal coordination   : angle       1.30880 (    6)
  covalent geometry    : bond        0.00343 ( 8794)
  covalent geometry    : angle       0.67063 (11938)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 185
  time to evaluate  : 1.294 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7433 (m-80) cc_final: 0.6914 (m-80)
REVERT: A  217 TYR cc_start: 0.5786 (p90) cc_final: 0.5183 (p90)
REVERT: A  380 MET cc_start: 0.8695 (ttp) cc_final: 0.7834 (ppp)
REVERT: A  456 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7186 (t80)
REVERT: A  759 SER cc_start: 0.8702 (p) cc_final: 0.8500 (m)
REVERT: A  822 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7099 (tm-30)
REVERT: A  889 ARG cc_start: 0.7993 (mtt90) cc_final: 0.7349 (mtt-85)
REVERT: B   82 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8734 (tptt)
REVERT: C   27 LYS cc_start: 0.6398 (OUTLIER) cc_final: 0.6129 (pttt)
REVERT: C   31 GLN cc_start: 0.7578 (mt0) cc_final: 0.7170 (mt0)
  outliers start: 35
  outliers final: 30
  residues processed: 210
  average time/residue: 0.2723
  time to fit residues: 79.1668
Evaluate side-chains
  210 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 178
  time to evaluate  : 1.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  468 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  788 TYR
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   27 LYS
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  165 LYS
Chi-restraints excluded: chain D residue  167 VAL
Chi-restraints excluded: chain D residue  189 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 1 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0770
   chunk 83 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 79 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 781 ASN
C  19 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.138965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.112935 restraints weight = 17227.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.116143 restraints weight = 9720.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.118360 restraints weight = 6659.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8802  Z= 0.139
  Angle     :  0.666  10.570  11944  Z= 0.343
  Chirality :  0.046   0.182   1350
  Planarity :  0.004   0.048   1517
  Dihedral  :  5.185  59.342   1174
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 24.19 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.25), residues: 1060
  helix:  0.53 (0.23), residues: 505
  sheet: -0.92 (0.49), residues: 94
  loop : -1.73 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 154 
 HIS   0.005   0.001   HIS A 309 
 PHE   0.022   0.001   PHE A 340 
 TYR   0.020   0.001   TYR A 453 
 ARG   0.005   0.000   ARG B 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04939 (  396)
  hydrogen bonds       : angle       5.29680 ( 1131)
  metal coordination   : bond        0.00979 (    8)
  metal coordination   : angle       1.27151 (    6)
  covalent geometry    : bond        0.00305 ( 8794)
  covalent geometry    : angle       0.66535 (11938)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 193
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7399 (m-80) cc_final: 0.6847 (m-80)
REVERT: A  456 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7260 (t80)
REVERT: A  822 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7149 (tm-30)
REVERT: A  865 ASP cc_start: 0.7215 (t70) cc_final: 0.6341 (m-30)
REVERT: A  882 HIS cc_start: 0.7829 (m170) cc_final: 0.7565 (m90)
REVERT: A  889 ARG cc_start: 0.7980 (mtt90) cc_final: 0.7317 (mtt-85)
REVERT: B   97 LYS cc_start: 0.8202 (tmtt) cc_final: 0.7692 (tttm)
REVERT: D  189 LEU cc_start: 0.4078 (OUTLIER) cc_final: 0.3862 (tt)
  outliers start: 35
  outliers final: 29
  residues processed: 218
  average time/residue: 0.2843
  time to fit residues: 84.9969
Evaluate side-chains
  208 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 177
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  468 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  782 PHE
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  167 VAL
Chi-restraints excluded: chain D residue  189 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 102 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 45 optimal weight:    0.2980
   chunk 20 optimal weight:    0.8980
   chunk 54 optimal weight:   20.0000
   chunk 61 optimal weight:   10.0000
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 381 HIS
A 572 HIS
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.140167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.114136 restraints weight = 17227.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.117482 restraints weight = 9664.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.119708 restraints weight = 6563.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.4292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8802  Z= 0.139
  Angle     :  0.676   9.919  11944  Z= 0.349
  Chirality :  0.046   0.198   1350
  Planarity :  0.004   0.060   1517
  Dihedral  :  5.179  57.964   1174
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 24.82 %
    Favored  : 71.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.25), residues: 1060
  helix:  0.56 (0.23), residues: 505
  sheet: -0.78 (0.50), residues: 94
  loop : -1.69 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 617 
 HIS   0.005   0.001   HIS A 256 
 PHE   0.022   0.001   PHE D  92 
 TYR   0.019   0.001   TYR A 453 
 ARG   0.007   0.001   ARG A 836 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04893 (  396)
  hydrogen bonds       : angle       5.25587 ( 1131)
  metal coordination   : bond        0.00911 (    8)
  metal coordination   : angle       1.15027 (    6)
  covalent geometry    : bond        0.00306 ( 8794)
  covalent geometry    : angle       0.67564 (11938)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 186
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7335 (m-80) cc_final: 0.6786 (m-80)
REVERT: A  258 ASP cc_start: 0.7525 (m-30) cc_final: 0.7045 (p0)
REVERT: A  265 TYR cc_start: 0.7316 (m-80) cc_final: 0.6984 (m-80)
REVERT: A  456 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7240 (t80)
REVERT: A  782 PHE cc_start: 0.6253 (OUTLIER) cc_final: 0.5960 (t80)
REVERT: A  805 LEU cc_start: 0.8015 (tt) cc_final: 0.7361 (pt)
REVERT: A  822 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7137 (tm-30)
REVERT: A  889 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7268 (mtt-85)
REVERT: B   90 MET cc_start: 0.8335 (tmm) cc_final: 0.7919 (tmm)
REVERT: B   97 LYS cc_start: 0.8235 (tmtt) cc_final: 0.7803 (tttm)
REVERT: D  139 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7779 (ptpp)
  outliers start: 34
  outliers final: 30
  residues processed: 211
  average time/residue: 0.3328
  time to fit residues: 97.4416
Evaluate side-chains
  212 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 180
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  456 TYR
Chi-restraints excluded: chain A residue  468 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  498 LEU
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  782 PHE
Chi-restraints excluded: chain A residue  788 TYR
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  167 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 74 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 73 optimal weight:    0.2980
   chunk 75 optimal weight:    7.9990
   chunk 101 optimal weight:    0.0670
   chunk 35 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    0.7920

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

Flipped N/Q/H residues before XYZ refinement:
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.141471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.115986 restraints weight = 17489.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.119432 restraints weight = 9756.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.121698 restraints weight = 6570.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.4408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8802  Z= 0.141
  Angle     :  0.696   9.963  11944  Z= 0.354
  Chirality :  0.046   0.215   1350
  Planarity :  0.004   0.058   1517
  Dihedral  :  5.106  56.991   1174
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 26.18 %
    Favored  : 70.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.25), residues: 1060
  helix:  0.65 (0.23), residues: 505
  sheet: -1.03 (0.53), residues: 84
  loop : -1.63 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 617 
 HIS   0.006   0.001   HIS A 381 
 PHE   0.026   0.001   PHE D  92 
 TYR   0.016   0.001   TYR A 453 
 ARG   0.007   0.001   ARG A 836 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04860 (  396)
  hydrogen bonds       : angle       5.21367 ( 1131)
  metal coordination   : bond        0.00912 (    8)
  metal coordination   : angle       1.05710 (    6)
  covalent geometry    : bond        0.00312 ( 8794)
  covalent geometry    : angle       0.69590 (11938)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5024.16 seconds
wall clock time: 93 minutes 30.23 seconds (5610.23 seconds total)