Starting phenix.real_space_refine
on Thu Mar 13 02:41:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bw4_30226/03_2025/7bw4_30226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bw4_30226/03_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_30226/03_2025/7bw4_30226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bw4_30226/03_2025/7bw4_30226.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bw4_30226/03_2025/7bw4_30226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bw4_30226/03_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-5624/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: 5.72, per 1000 atoms: 0.66
  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: 2.29
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  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: 1.02
  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: 2.37

  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:             0.670
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.590
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.720
-------------------------------------------------------------------------------
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      :  0.004   0.041   8794  Z= 0.245
  Angle     :  0.655   8.651  11938  Z= 0.421
  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 

*********************** 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  : 1.027 
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: 0.2541
  time to fit residues: 88.8890
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  : 1.093 
-------------------------------------------------------------------------------
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:    5.9990
   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   8794  Z= 0.201
  Angle     :  0.643   9.442  11938  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 

*********************** 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  : 1.004 
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: 0.2332
  time to fit residues: 69.8421
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  : 0.960 
-------------------------------------------------------------------------------
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   0.036   8794  Z= 0.268
  Angle     :  0.656   8.924  11938  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 

*********************** 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  : 1.187 
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: 0.2774
  time to fit residues: 78.7748
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  : 0.930 
-------------------------------------------------------------------------------
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:    0.9990
   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:    1.7584

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.136130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.109441 restraints weight = 17017.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.112667 restraints weight = 9624.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.114833 restraints weight = 6596.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8794  Z= 0.237
  Angle     :  0.630   8.823  11938  Z= 0.341
  Chirality :  0.045   0.165   1350
  Planarity :  0.004   0.050   1517
  Dihedral  :  5.327  54.788   1174
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 17.46 %
    Favored  : 78.55 %
  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: -1.25 (0.25), residues: 1060
  helix:  0.32 (0.23), residues: 508
  sheet: -1.53 (0.46), residues: 89
  loop : -2.00 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 154 
 HIS   0.004   0.001   HIS A 309 
 PHE   0.015   0.001   PHE B 147 
 TYR   0.031   0.002   TYR A 453 
 ARG   0.005   0.000   ARG A 836 

*********************** 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
  216 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 178
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7249 (m-80) cc_final: 0.6737 (m-80)
REVERT: A  456 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7142 (t80)
REVERT: A  500 LYS cc_start: 0.6246 (mttp) cc_final: 0.5794 (tttm)
REVERT: A  575 LEU cc_start: 0.7804 (tp) cc_final: 0.7442 (tt)
REVERT: A  822 GLN cc_start: 0.7813 (tm-30) cc_final: 0.6931 (tm-30)
REVERT: A  825 ASP cc_start: 0.7030 (p0) cc_final: 0.6118 (p0)
REVERT: A  889 ARG cc_start: 0.8110 (mtt90) cc_final: 0.7410 (mmt90)
REVERT: C   27 LYS cc_start: 0.6436 (OUTLIER) cc_final: 0.6145 (pttt)
REVERT: C   31 GLN cc_start: 0.7597 (mt0) cc_final: 0.7263 (mt0)
REVERT: C   38 ASP cc_start: 0.7709 (t0) cc_final: 0.7468 (t0)
REVERT: D  139 LYS cc_start: 0.8299 (mmtt) cc_final: 0.8072 (ptpt)
  outliers start: 38
  outliers final: 24
  residues processed: 203
  average time/residue: 0.2296
  time to fit residues: 64.1581
Evaluate side-chains
  190 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 164
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
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  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:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 88 optimal weight:    8.9990
   chunk 35 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    3.9788

-------------------------------------------------------------------------------
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
A 810 HIS
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.129709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.103066 restraints weight = 17316.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.106046 restraints weight = 10039.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.108059 restraints weight = 6983.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   8794  Z= 0.441
  Angle     :  0.774   8.808  11938  Z= 0.418
  Chirality :  0.050   0.181   1350
  Planarity :  0.005   0.054   1517
  Dihedral  :  5.776  51.660   1174
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.60 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 19.98 %
    Favored  : 75.50 %
  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: -1.55 (0.24), residues: 1060
  helix:  0.02 (0.22), residues: 504
  sheet: -1.34 (0.55), residues: 74
  loop : -2.13 (0.24), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 154 
 HIS   0.005   0.001   HIS A 642 
 PHE   0.022   0.002   PHE A 766 
 TYR   0.028   0.002   TYR A 453 
 ARG   0.005   0.001   ARG B  80 

*********************** 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
  220 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 177
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7394 (m-80) cc_final: 0.6966 (m-80)
REVERT: A  497 ASN cc_start: 0.8165 (t0) cc_final: 0.7916 (t0)
REVERT: A  663 LEU cc_start: 0.8750 (tp) cc_final: 0.8482 (tt)
REVERT: A  822 GLN cc_start: 0.7920 (tm-30) cc_final: 0.6990 (tm-30)
REVERT: A  825 ASP cc_start: 0.7155 (p0) cc_final: 0.6347 (p0)
REVERT: A  889 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7540 (mtt-85)
REVERT: C   27 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6434 (pttt)
REVERT: C   31 GLN cc_start: 0.7565 (mt0) cc_final: 0.7241 (mt0)
  outliers start: 43
  outliers final: 31
  residues processed: 206
  average time/residue: 0.2541
  time to fit residues: 71.4548
Evaluate side-chains
  196 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 164
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
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  299 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  353 VAL
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  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 B residue   83 VAL
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  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:    0.9990
   chunk 103 optimal weight:   10.0000
   chunk 97 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 80 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 58 optimal weight:    7.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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**
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.138605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.112727 restraints weight = 16982.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.116070 restraints weight = 9716.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.118252 restraints weight = 6638.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.3662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8794  Z= 0.185
  Angle     :  0.626   9.474  11938  Z= 0.333
  Chirality :  0.044   0.173   1350
  Planarity :  0.004   0.051   1517
  Dihedral  :  5.348  58.780   1174
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 21.98 %
    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: -1.06 (0.25), residues: 1060
  helix:  0.37 (0.23), residues: 505
  sheet: -1.24 (0.55), residues: 74
  loop : -1.80 (0.26), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  29 
 HIS   0.004   0.001   HIS C  36 
 PHE   0.011   0.001   PHE A 287 
 TYR   0.027   0.001   TYR A 453 
 ARG   0.004   0.000   ARG B  80 

*********************** 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
  233 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 200
  time to evaluate  : 1.045 
Fit side-chains
REVERT: A   35 PHE cc_start: 0.7317 (m-80) cc_final: 0.6799 (m-80)
REVERT: A  217 TYR cc_start: 0.5747 (p90) cc_final: 0.5132 (p90)
REVERT: A  456 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7168 (t80)
REVERT: A  668 MET cc_start: 0.7486 (tpt) cc_final: 0.7226 (tpt)
REVERT: A  759 SER cc_start: 0.8791 (p) cc_final: 0.8508 (m)
REVERT: A  811 GLU cc_start: 0.7036 (tp30) cc_final: 0.6307 (mm-30)
REVERT: A  822 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7018 (tm-30)
REVERT: A  825 ASP cc_start: 0.7058 (p0) cc_final: 0.6448 (p0)
REVERT: A  889 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7370 (mtt-85)
REVERT: B   82 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8690 (tptt)
REVERT: B   94 MET cc_start: 0.7020 (ptm) cc_final: 0.6763 (ptp)
REVERT: C   19 GLN cc_start: 0.8207 (tp40) cc_final: 0.7970 (tp40)
REVERT: C   27 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.6141 (pttt)
REVERT: C   31 GLN cc_start: 0.7646 (mt0) cc_final: 0.7209 (mt0)
REVERT: C   38 ASP cc_start: 0.7710 (t0) cc_final: 0.7436 (t0)
REVERT: D  108 ASN cc_start: 0.8194 (m-40) cc_final: 0.7966 (m110)
REVERT: D  129 MET cc_start: 0.6846 (tpp) cc_final: 0.6613 (tpp)
  outliers start: 33
  outliers final: 23
  residues processed: 221
  average time/residue: 0.2595
  time to fit residues: 81.2033
Evaluate side-chains
  204 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 179
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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  763 VAL
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  928 HIS
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  189 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 10 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0870
   chunk 63 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 72 optimal weight:    7.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.139791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.114129 restraints weight = 17234.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.117466 restraints weight = 9780.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.119667 restraints weight = 6667.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8794  Z= 0.180
  Angle     :  0.630  10.036  11938  Z= 0.333
  Chirality :  0.045   0.218   1350
  Planarity :  0.004   0.049   1517
  Dihedral  :  5.204  59.288   1174
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 23.03 %
    Favored  : 73.29 %
  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:  0.59 (0.23), residues: 505
  sheet: -0.92 (0.50), residues: 94
  loop : -1.80 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 154 
 HIS   0.005   0.001   HIS A 309 
 PHE   0.026   0.001   PHE D  92 
 TYR   0.023   0.001   TYR A 453 
 ARG   0.004   0.000   ARG B 190 

*********************** 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
  229 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 194
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7380 (m-80) cc_final: 0.6851 (m-80)
REVERT: A  217 TYR cc_start: 0.5728 (p90) cc_final: 0.5156 (p90)
REVERT: A  456 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7234 (t80)
REVERT: A  822 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7044 (tm-30)
REVERT: A  882 HIS cc_start: 0.7801 (m170) cc_final: 0.7533 (m90)
REVERT: A  889 ARG cc_start: 0.7979 (mtt90) cc_final: 0.7287 (mtt-85)
REVERT: B   82 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8731 (tptt)
REVERT: B   94 MET cc_start: 0.7039 (ptm) cc_final: 0.6740 (ptp)
REVERT: D   92 PHE cc_start: 0.8443 (m-80) cc_final: 0.8166 (m-80)
REVERT: D  139 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7823 (ptpp)
  outliers start: 35
  outliers final: 27
  residues processed: 221
  average time/residue: 0.2152
  time to fit residues: 66.2871
Evaluate side-chains
  206 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 178
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
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  338 VAL
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  386 ASN
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  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  788 TYR
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  928 HIS
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
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:    6.9990
   chunk 84 optimal weight:    6.9990
   chunk 104 optimal weight:    6.9990
   chunk 22 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0370
   chunk 14 optimal weight:    0.6980
   chunk 79 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 87 optimal weight:    7.9990
   overall best weight:    1.8662

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

Flipped N/Q/H residues before XYZ refinement:
** A 386 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 = 0.3982 r_free = 0.3982 target = 0.136422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.110286 restraints weight = 17593.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.113559 restraints weight = 10025.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.115728 restraints weight = 6874.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8794  Z= 0.258
  Angle     :  0.684   9.546  11938  Z= 0.360
  Chirality :  0.047   0.209   1350
  Planarity :  0.004   0.056   1517
  Dihedral  :  5.313  57.989   1174
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 23.97 %
    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: -0.92 (0.25), residues: 1060
  helix:  0.48 (0.23), residues: 508
  sheet: -0.66 (0.54), residues: 84
  loop : -1.86 (0.26), residues: 468

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   0.023   0.002   PHE D  92 
 TYR   0.025   0.002   TYR A 453 
 ARG   0.004   0.001   ARG B 190 

*********************** 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
  221 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 184
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7353 (m-80) cc_final: 0.6884 (m-80)
REVERT: A  217 TYR cc_start: 0.5817 (p90) cc_final: 0.5226 (p90)
REVERT: A  456 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7164 (t80)
REVERT: A  575 LEU cc_start: 0.7860 (tp) cc_final: 0.7592 (tt)
REVERT: A  822 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7128 (tm-30)
REVERT: A  889 ARG cc_start: 0.8027 (mtt90) cc_final: 0.7391 (mtt-85)
REVERT: B   82 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8737 (tptt)
REVERT: B   94 MET cc_start: 0.7097 (ptm) cc_final: 0.6788 (ptp)
REVERT: C   31 GLN cc_start: 0.7606 (mt0) cc_final: 0.7316 (mt0)
REVERT: D  139 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7824 (ptpp)
  outliers start: 37
  outliers final: 32
  residues processed: 210
  average time/residue: 0.2044
  time to fit residues: 58.5453
Evaluate side-chains
  210 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 177
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  226 THR
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  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 A residue  928 HIS
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  122 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 83 optimal weight:    9.9990
   chunk 46 optimal weight:    0.5980
   chunk 105 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9990
   chunk 79 optimal weight:    8.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 781 ASN
** 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 = 0.3974 r_free = 0.3974 target = 0.135694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.109788 restraints weight = 17404.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.113017 restraints weight = 9866.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.115161 restraints weight = 6736.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8794  Z= 0.262
  Angle     :  0.693   9.566  11938  Z= 0.362
  Chirality :  0.047   0.215   1350
  Planarity :  0.004   0.054   1517
  Dihedral  :  5.393  58.625   1174
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 24.40 %
    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: -1.03 (0.25), residues: 1060
  helix:  0.41 (0.23), residues: 510
  sheet: -1.11 (0.53), residues: 84
  loop : -1.85 (0.26), residues: 466

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   0.027   0.002   PHE D  92 
 TYR   0.024   0.001   TYR A 453 
 ARG   0.005   0.001   ARG B 190 

*********************** 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
  219 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 181
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7362 (m-80) cc_final: 0.6886 (m-80)
REVERT: A  163 TYR cc_start: 0.8902 (p90) cc_final: 0.8667 (p90)
REVERT: A  217 TYR cc_start: 0.5800 (p90) cc_final: 0.5218 (p90)
REVERT: A  456 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7048 (t80)
REVERT: A  575 LEU cc_start: 0.7816 (tp) cc_final: 0.7507 (tt)
REVERT: A  822 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7152 (tm-30)
REVERT: A  889 ARG cc_start: 0.8040 (mtt90) cc_final: 0.7392 (mtt-85)
REVERT: C   31 GLN cc_start: 0.7659 (mt0) cc_final: 0.7375 (mt0)
REVERT: D   92 PHE cc_start: 0.8450 (m-80) cc_final: 0.8245 (m-80)
REVERT: D  139 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7840 (ptpp)
  outliers start: 38
  outliers final: 31
  residues processed: 207
  average time/residue: 0.2165
  time to fit residues: 61.1376
Evaluate side-chains
  205 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  226 THR
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  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  829 LEU
Chi-restraints excluded: chain A residue  928 HIS
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  122 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:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.3184

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.138080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.112220 restraints weight = 17288.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.115547 restraints weight = 9816.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.117723 restraints weight = 6683.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.4154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8794  Z= 0.221
  Angle     :  0.686   9.513  11938  Z= 0.356
  Chirality :  0.046   0.204   1350
  Planarity :  0.004   0.053   1517
  Dihedral  :  5.358  59.744   1174
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 25.66 %
    Favored  : 71.08 %
  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: -0.98 (0.25), residues: 1060
  helix:  0.46 (0.23), residues: 510
  sheet: -1.14 (0.53), residues: 84
  loop : -1.83 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 154 
 HIS   0.005   0.001   HIS A 256 
 PHE   0.026   0.001   PHE D  92 
 TYR   0.025   0.001   TYR A 453 
 ARG   0.005   0.000   ARG B 190 

********************** 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
  214 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 183
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.7392 (m-80) cc_final: 0.6920 (m-80)
REVERT: A  217 TYR cc_start: 0.5703 (p90) cc_final: 0.5147 (p90)
REVERT: A  258 ASP cc_start: 0.7592 (m-30) cc_final: 0.7199 (p0)
REVERT: A  265 TYR cc_start: 0.7247 (m-80) cc_final: 0.6935 (m-80)
REVERT: A  456 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7207 (t80)
REVERT: A  805 LEU cc_start: 0.8129 (tt) cc_final: 0.7564 (pt)
REVERT: A  822 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7179 (tm-30)
REVERT: A  889 ARG cc_start: 0.7960 (mtt90) cc_final: 0.7330 (mtt-85)
REVERT: B   94 MET cc_start: 0.6974 (ptm) cc_final: 0.6636 (ptp)
REVERT: D   92 PHE cc_start: 0.8427 (m-80) cc_final: 0.8211 (m-80)
REVERT: D  139 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7813 (ptpp)
  outliers start: 31
  outliers final: 28
  residues processed: 204
  average time/residue: 0.2029
  time to fit residues: 57.3947
Evaluate side-chains
  205 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 176
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  804 ASP
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  928 HIS
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue   20 LEU
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  167 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 75 optimal weight:    7.9990
   chunk 101 optimal weight:    0.0270
   chunk 35 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0020
   chunk 102 optimal weight:    5.9990
   overall best weight:    1.7650

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.136889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.110853 restraints weight = 17463.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.114156 restraints weight = 9901.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.116328 restraints weight = 6721.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.4200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8794  Z= 0.254
  Angle     :  0.715  10.868  11938  Z= 0.368
  Chirality :  0.047   0.236   1350
  Planarity :  0.004   0.053   1517
  Dihedral  :  5.388  59.978   1174
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 25.24 %
    Favored  : 71.08 %
  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: -1.09 (0.25), residues: 1060
  helix:  0.39 (0.23), residues: 511
  sheet: -1.43 (0.55), residues: 78
  loop : -1.86 (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   0.025   0.002   PHE D  92 
 TYR   0.024   0.001   TYR A 453 
 ARG   0.005   0.001   ARG B 190 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3045.53 seconds
wall clock time: 55 minutes 16.78 seconds (3316.78 seconds total)