Starting phenix.real_space_refine
on Thu Mar 13 18:04:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zkb_14761/03_2025/7zkb_14761.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zkb_14761/03_2025/7zkb_14761.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zkb_14761/03_2025/7zkb_14761.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zkb_14761/03_2025/7zkb_14761.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zkb_14761/03_2025/7zkb_14761.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zkb_14761/03_2025/7zkb_14761.cif"
  }
  resolution = 4.7
  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=   0.002 sd=   0.023
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: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    5806      2.51       5
     N    1541      2.21       5
     O    1657      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 9043
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1157, 8968
          Classifications: {'peptide': 1157}
          Link IDs: {'PTRANS': 29, 'TRANS': 1127}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 75
          Unusual residues: {'JIZ': 1, 'JJI': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.07, per 1000 atoms: 0.67
  Number of scatterers: 9043
  At special positions: 0
  Unit cell: (77.004, 112.158, 148.149, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1657      8.00
     N    1541      7.00
     C    5806      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.79
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 5 sheets defined
      65.5% alpha, 2.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 83
      removed outlier: 4.290A  pdb=" N   LEU A  64 " --> pdb=" O   HIS A  60 " (cutoff:3.500A)
      Proline residue:  A  65  - end of helix
    Processing helix  chain 'A' and resid 86 through 92
    Processing helix  chain 'A' and resid 98 through 152
    Processing helix  chain 'A' and resid 155 through 161
      removed outlier: 3.982A  pdb=" N   PHE A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 207
      removed outlier: 4.025A  pdb=" N   VAL A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   SER A 176 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
      removed outlier: 5.440A  pdb=" N   ILE A 186 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   PHE A 190 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   GLN A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 256
      Proline residue:  A 219  - end of helix
      removed outlier: 3.672A  pdb=" N   ALA A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ALA A 256 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 264
    Processing helix  chain 'A' and resid 265 through 319
      removed outlier: 4.250A  pdb=" N   GLU A 271 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ARG A 272 " --> pdb=" O   LYS A 268 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ALA A 280 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG A 282 " --> pdb=" O   GLU A 278 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   LEU A 283 " --> pdb=" O   GLU A 279 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   SER A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   LEU A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER A 315 " --> pdb=" O   TRP A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 343
      removed outlier: 3.512A  pdb=" N   VAL A 330 " --> pdb=" O   GLN A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 365
    Processing helix  chain 'A' and resid 430 through 435
      removed outlier: 3.551A  pdb=" N   LEU A 435 " --> pdb=" O   THR A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 465
    Processing helix  chain 'A' and resid 479 through 486
    Processing helix  chain 'A' and resid 492 through 501
    Processing helix  chain 'A' and resid 528 through 544
      removed outlier: 3.925A  pdb=" N   ARG A 534 " --> pdb=" O   GLY A 530 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASN A 544 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 576
      removed outlier: 3.617A  pdb=" N   GLY A 575 " --> pdb=" O   LYS A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 591
      removed outlier: 3.756A  pdb=" N   ARG A 589 " --> pdb=" O   LEU A 585 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ASN A 590 " --> pdb=" O   SER A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 701
      removed outlier: 4.002A  pdb=" N   SER A 701 " --> pdb=" O   LEU A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 719
      removed outlier: 4.717A  pdb=" N   VAL A 709 " --> pdb=" O   PRO A 705 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   GLY A 710 " --> pdb=" O   TYR A 706 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ILE A 711 " --> pdb=" O   PHE A 707 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   PHE A 712 " --> pdb=" O   VAL A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 737
      removed outlier: 3.836A  pdb=" N   ALA A 723 " --> pdb=" O   GLY A 719 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   PHE A 735 " --> pdb=" O   VAL A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 801
      removed outlier: 3.677A  pdb=" N   SER A 748 " --> pdb=" O   GLN A 744 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LYS A 775 " --> pdb=" O   PHE A 771 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASP A 796 " --> pdb=" O   MET A 792 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   VAL A 797 " --> pdb=" O   LEU A 793 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   SER A 798 " --> pdb=" O   ARG A 794 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   TRP A 799 " --> pdb=" O   GLN A 795 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   PHE A 800 " --> pdb=" O   ASP A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 806 through 816
    Processing helix  chain 'A' and resid 817 through 849
      removed outlier: 3.607A  pdb=" N   GLY A 826 " --> pdb=" O   LYS A 822 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   ARG A 828 " --> pdb=" O   ALA A 824 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   LEU A 829 " --> pdb=" O   THR A 825 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ILE A 832 " --> pdb=" O   ARG A 828 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 852 through 899
      removed outlier: 3.719A  pdb=" N   LEU A 856 " --> pdb=" O   GLN A 852 " (cutoff:3.500A)
      Proline residue:  A 862  - end of helix
      removed outlier: 3.809A  pdb=" N   LYS A 883 " --> pdb=" O   ALA A 879 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   LYS A 884 " --> pdb=" O   LEU A 880 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLY A 888 " --> pdb=" O   LYS A 884 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   SER A 889 " --> pdb=" O   GLU A 885 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ILE A 892 " --> pdb=" O   GLY A 888 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   GLU A 895 " --> pdb=" O   LYS A 891 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 906
    Processing helix  chain 'A' and resid 909 through 962
      removed outlier: 3.668A  pdb=" N   GLU A 913 " --> pdb=" O   GLU A 909 " (cutoff:3.500A)
      Proline residue:  A 923  - end of helix
    Processing helix  chain 'A' and resid 966 through 991
      removed outlier: 3.507A  pdb=" N   GLY A 985 " --> pdb=" O   ALA A 981 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA A 991 " --> pdb=" O   VAL A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1010
    Processing helix  chain 'A' and resid 1072 through 1078
      removed outlier: 3.750A  pdb=" N   VAL A1076 " --> pdb=" O   LYS A1072 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1098 through 1100
      No H-bonds generated for 'chain 'A' and resid 1098 through 1100'
    Processing helix  chain 'A' and resid 1101 through 1108
      removed outlier: 3.648A  pdb=" N   GLN A1108 " --> pdb=" O   TRP A1104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1122 through 1129
    Processing helix  chain 'A' and resid 1140 through 1148
    Processing helix  chain 'A' and resid 1150 through 1155
    Processing helix  chain 'A' and resid 1175 through 1188
      removed outlier: 3.700A  pdb=" N   ARG A1179 " --> pdb=" O   GLY A1175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1204 through 1221
    Processing helix  chain 'A' and resid 1229 through 1236
    Processing helix  chain 'A' and resid 1250 through 1255
      removed outlier: 3.719A  pdb=" N   GLN A1254 " --> pdb=" O   HIS A1250 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 391
    Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 395
    Processing sheet with id=AA3, first strand: chain 'A' and resid 466 through 468
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1031 through 1032
      removed outlier: 3.938A  pdb=" N   PHE A1091 " --> pdb=" O   GLN A1032 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1109 through 1112
      removed outlier: 6.066A  pdb=" N   LEU A1193 " --> pdb=" O   ILE A1224 " (cutoff:3.500A)

    559 hydrogen bonds defined for protein.
    1668 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: 3.39

  Time building geometry restraints manager: 3.08 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 1481
        1.31 -     1.46: 2772
        1.46 -     1.60: 4886
        1.60 -     1.74: 12
        1.74 -     1.89: 63
  Bond restraints: 9214
  Sorted by residual:
  bond pdb=" N2  JJI A1402 "
       pdb=" O22 JJI A1402 "
    ideal  model  delta    sigma   weight residual
    1.204  1.405 -0.201 2.00e-02 2.50e+03 1.01e+02
  bond pdb=" N4  JJI A1402 "
       pdb=" O41 JJI A1402 "
    ideal  model  delta    sigma   weight residual
    1.206  1.404 -0.198 2.00e-02 2.50e+03 9.84e+01
  bond pdb=" N2  JJI A1402 "
       pdb=" O21 JJI A1402 "
    ideal  model  delta    sigma   weight residual
    1.206  1.404 -0.198 2.00e-02 2.50e+03 9.76e+01
  bond pdb=" N4  JJI A1402 "
       pdb=" O42 JJI A1402 "
    ideal  model  delta    sigma   weight residual
    1.207  1.403 -0.196 2.00e-02 2.50e+03 9.62e+01
  bond pdb=" S   JJI A1402 "
       pdb=" S04 JJI A1402 "
    ideal  model  delta    sigma   weight residual
    2.053  1.888  0.165 2.00e-02 2.50e+03 6.83e+01
  ... (remaining 9209 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.04: 12312
        4.04 -     8.08: 134
        8.08 -    12.12: 10
       12.12 -    16.17: 2
       16.17 -    20.21: 3
  Bond angle restraints: 12461
  Sorted by residual:
  angle pdb=" N   TYR A 306 "
        pdb=" CA  TYR A 306 "
        pdb=" C   TYR A 306 "
      ideal   model   delta    sigma   weight residual
     111.28   98.42   12.86 1.09e+00 8.42e-01 1.39e+02
  angle pdb=" N   VAL A 249 "
        pdb=" CA  VAL A 249 "
        pdb=" C   VAL A 249 "
      ideal   model   delta    sigma   weight residual
     110.62  102.65    7.97 1.02e+00 9.61e-01 6.11e+01
  angle pdb=" C18 JJI A1402 "
        pdb=" S04 JJI A1402 "
        pdb=" S   JJI A1402 "
      ideal   model   delta    sigma   weight residual
     102.75  122.96  -20.21 3.00e+00 1.11e-01 4.54e+01
  angle pdb=" O   ALA A 244 "
        pdb=" C   ALA A 244 "
        pdb=" N   LYS A 245 "
      ideal   model   delta    sigma   weight residual
     122.22  114.95    7.27 1.17e+00 7.31e-01 3.86e+01
  angle pdb=" C13 JIZ A1401 "
        pdb=" C15 JIZ A1401 "
        pdb=" N01 JIZ A1401 "
      ideal   model   delta    sigma   weight residual
     114.63  131.99  -17.36 3.00e+00 1.11e-01 3.35e+01
  ... (remaining 12456 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.47: 5105
       22.47 -    44.94: 326
       44.94 -    67.40: 32
       67.40 -    89.87: 17
       89.87 -   112.34: 12
  Dihedral angle restraints: 5492
    sinusoidal: 2181
      harmonic: 3311
  Sorted by residual:
  dihedral pdb=" C   PHE A 339 "
           pdb=" N   PHE A 339 "
           pdb=" CA  PHE A 339 "
           pdb=" CB  PHE A 339 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.42  -11.18     0      2.50e+00 1.60e-01 2.00e+01
  dihedral pdb=" C   ASN A 276 "
           pdb=" N   ASN A 276 "
           pdb=" CA  ASN A 276 "
           pdb=" CB  ASN A 276 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.39   10.79     0      2.50e+00 1.60e-01 1.86e+01
  dihedral pdb=" CA  GLU A1139 "
           pdb=" C   GLU A1139 "
           pdb=" N   GLU A1140 "
           pdb=" CA  GLU A1140 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.79   19.21     0      5.00e+00 4.00e-02 1.48e+01
  ... (remaining 5489 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1186
       0.071 -    0.143: 186
       0.143 -    0.214: 38
       0.214 -    0.286: 9
       0.286 -    0.357: 7
  Chirality restraints: 1426
  Sorted by residual:
  chirality pdb=" CA  LYS A 245 "
            pdb=" N   LYS A 245 "
            pdb=" C   LYS A 245 "
            pdb=" CB  LYS A 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CA  PHE A 339 "
            pdb=" N   PHE A 339 "
            pdb=" C   PHE A 339 "
            pdb=" CB  PHE A 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.93e+00
  chirality pdb=" CA  TYR A 306 "
            pdb=" N   TYR A 306 "
            pdb=" C   TYR A 306 "
            pdb=" CB  TYR A 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.68e+00
  ... (remaining 1423 not shown)

  Planarity restraints: 1586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 244 "   -0.026 2.00e-02 2.50e+03   4.91e-02 2.41e+01
        pdb=" C   ALA A 244 "    0.085 2.00e-02 2.50e+03
        pdb=" O   ALA A 244 "   -0.030 2.00e-02 2.50e+03
        pdb=" N   LYS A 245 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 247 "    0.017 2.00e-02 2.50e+03   3.48e-02 1.21e+01
        pdb=" C   GLY A 247 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   GLY A 247 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ALA A 248 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 301 "   -0.017 2.00e-02 2.50e+03   3.43e-02 1.18e+01
        pdb=" C   LEU A 301 "    0.059 2.00e-02 2.50e+03
        pdb=" O   LEU A 301 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ILE A 302 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1583 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1448
        2.76 -     3.29: 9792
        3.29 -     3.83: 14853
        3.83 -     4.36: 16865
        4.36 -     4.90: 27233
  Nonbonded interactions: 70191
  Sorted by model distance:
  nonbonded pdb=" O   TYR A1129 "
            pdb=" ND2 ASN A1132 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" O   GLY A 427 "
            pdb=" OG1 THR A 431 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG  SER A1122 "
            pdb=" O   TYR A1161 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ALA A  79 "
            pdb=" CG  GLN A  83 "
     model   vdw
     2.246 3.440
  nonbonded pdb=" O   MET A  74 "
            pdb=" OG  SER A  77 "
     model   vdw
     2.260 3.040
  ... (remaining 70186 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.450
  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:          0.410
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     25.120
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.060
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
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      :  0.008   0.201   9214  Z= 0.564
  Angle     :  1.045  20.208  12461  Z= 0.643
  Chirality :  0.061   0.357   1426
  Planarity :  0.005   0.062   1586
  Dihedral  : 15.447 112.340   3370
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.80 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.07 (0.26), residues: 1153
  helix:  1.03 (0.20), residues: 711
  sheet: -0.11 (0.83), residues: 42
  loop : -1.74 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 704 
 HIS   0.004   0.000   HIS A1003 
 PHE   0.016   0.001   PHE A1038 
 TYR   0.017   0.002   TYR A 113 
 ARG   0.006   0.000   ARG A1134 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 244
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 MET cc_start: 0.7500 (tpp) cc_final: 0.7296 (mmt)
REVERT: A  127 ILE cc_start: 0.8749 (mt) cc_final: 0.8518 (mt)
REVERT: A  152 MET cc_start: 0.7790 (tpp) cc_final: 0.7519 (tmm)
REVERT: A  174 ASP cc_start: 0.7962 (m-30) cc_final: 0.7193 (m-30)
REVERT: A  259 THR cc_start: 0.9561 (p) cc_final: 0.9256 (p)
REVERT: A  263 PHE cc_start: 0.8357 (m-80) cc_final: 0.7986 (m-80)
REVERT: A  316 LEU cc_start: 0.8518 (mt) cc_final: 0.7809 (mt)
REVERT: A  364 ILE cc_start: 0.8642 (mp) cc_final: 0.8133 (tp)
REVERT: A  765 THR cc_start: 0.8773 (m) cc_final: 0.8571 (m)
REVERT: A  913 GLU cc_start: 0.7085 (tt0) cc_final: 0.6694 (tt0)
REVERT: A  968 GLU cc_start: 0.7206 (pp20) cc_final: 0.6880 (pp20)
REVERT: A 1062 LEU cc_start: 0.9358 (tp) cc_final: 0.9077 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 246
  average time/residue: 0.1857
  time to fit residues: 65.3457
Evaluate side-chains
  204 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 203
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    8.9990
   chunk 46 optimal weight:   20.0000
   chunk 90 optimal weight:    3.9990
   chunk 34 optimal weight:   20.0000
   chunk 54 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 504 ASN
A 566 GLN
A 737 ASN
A 878 GLN
** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1253 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.170594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.131093 restraints weight = 18983.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.132523 restraints weight = 14736.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.133864 restraints weight = 10488.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   9214  Z= 0.265
  Angle     :  0.660   6.917  12461  Z= 0.354
  Chirality :  0.043   0.196   1426
  Planarity :  0.005   0.071   1586
  Dihedral  : 12.295 105.590   1289
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  5.49 %
    Favored  : 94.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.02 (0.25), residues: 1153
  helix:  0.95 (0.20), residues: 707
  sheet:  0.26 (0.85), residues: 35
  loop : -1.76 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 704 
 HIS   0.004   0.001   HIS A 141 
 PHE   0.026   0.002   PHE A 755 
 TYR   0.017   0.002   TYR A 306 
 ARG   0.006   0.001   ARG A 485 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 234
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 MET cc_start: 0.8207 (mmm) cc_final: 0.7932 (mmm)
REVERT: A  152 MET cc_start: 0.8092 (tpp) cc_final: 0.7715 (mmm)
REVERT: A  174 ASP cc_start: 0.7815 (m-30) cc_final: 0.7598 (m-30)
REVERT: A  197 PHE cc_start: 0.8328 (m-80) cc_final: 0.8047 (m-80)
REVERT: A  259 THR cc_start: 0.9654 (p) cc_final: 0.9422 (p)
REVERT: A  263 PHE cc_start: 0.8647 (m-80) cc_final: 0.8237 (m-80)
REVERT: A  295 MET cc_start: 0.7999 (ttt) cc_final: 0.7349 (ttt)
REVERT: A  334 VAL cc_start: 0.9106 (t) cc_final: 0.8728 (m)
REVERT: A  436 MET cc_start: 0.9391 (mmp) cc_final: 0.9067 (mmm)
REVERT: A  465 ILE cc_start: 0.8650 (pt) cc_final: 0.8302 (mm)
REVERT: A  533 GLN cc_start: 0.8503 (pt0) cc_final: 0.8287 (tp-100)
REVERT: A  720 LEU cc_start: 0.9524 (mm) cc_final: 0.9320 (mm)
REVERT: A  765 THR cc_start: 0.8922 (m) cc_final: 0.8714 (m)
REVERT: A  796 ASP cc_start: 0.8026 (t0) cc_final: 0.7748 (m-30)
REVERT: A  797 VAL cc_start: 0.8462 (m) cc_final: 0.8010 (t)
REVERT: A  813 ARG cc_start: 0.8202 (tpt170) cc_final: 0.7885 (ttm170)
REVERT: A  821 VAL cc_start: 0.8113 (t) cc_final: 0.7605 (m)
REVERT: A  915 MET cc_start: 0.8129 (mpp) cc_final: 0.7755 (mpp)
REVERT: A  968 GLU cc_start: 0.7571 (pp20) cc_final: 0.7044 (pp20)
REVERT: A 1006 ARG cc_start: 0.7691 (ttt90) cc_final: 0.7317 (ttt90)
REVERT: A 1062 LEU cc_start: 0.9377 (tp) cc_final: 0.9147 (tp)
REVERT: A 1084 ASP cc_start: 0.8806 (p0) cc_final: 0.8603 (p0)
REVERT: A 1209 VAL cc_start: 0.9139 (t) cc_final: 0.8875 (p)
REVERT: A 1211 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8860 (pp30)
  outliers start: 4
  outliers final: 0
  residues processed: 235
  average time/residue: 0.2491
  time to fit residues: 84.7583
Evaluate side-chains
  199 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 1.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 105 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 41 optimal weight:   30.0000
   chunk 12 optimal weight:    0.9980
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
A 583 HIS
A 878 GLN
** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.170474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.128607 restraints weight = 19640.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.132473 restraints weight = 12950.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.135308 restraints weight = 9438.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9214  Z= 0.213
  Angle     :  0.614   7.625  12461  Z= 0.331
  Chirality :  0.041   0.162   1426
  Planarity :  0.004   0.060   1586
  Dihedral  : 11.765 104.002   1289
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.70 %
    Favored  : 96.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.02 (0.25), residues: 1153
  helix:  0.96 (0.19), residues: 716
  sheet:  0.11 (0.84), residues: 35
  loop : -1.83 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 704 
 HIS   0.004   0.001   HIS A1003 
 PHE   0.022   0.002   PHE A 755 
 TYR   0.020   0.002   TYR A 114 
 ARG   0.005   0.000   ARG A 485 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 224
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 MET cc_start: 0.8193 (mmm) cc_final: 0.7962 (mmm)
REVERT: A  152 MET cc_start: 0.8210 (tpp) cc_final: 0.7538 (mmm)
REVERT: A  154 GLN cc_start: 0.8708 (mt0) cc_final: 0.8476 (tt0)
REVERT: A  174 ASP cc_start: 0.8115 (m-30) cc_final: 0.7706 (m-30)
REVERT: A  259 THR cc_start: 0.9620 (p) cc_final: 0.9253 (p)
REVERT: A  295 MET cc_start: 0.7818 (ttt) cc_final: 0.7257 (ttt)
REVERT: A  436 MET cc_start: 0.9344 (mmp) cc_final: 0.9068 (mmm)
REVERT: A  465 ILE cc_start: 0.8634 (pt) cc_final: 0.8295 (mm)
REVERT: A  533 GLN cc_start: 0.8544 (pt0) cc_final: 0.8207 (tm-30)
REVERT: A  765 THR cc_start: 0.8917 (m) cc_final: 0.8702 (m)
REVERT: A  796 ASP cc_start: 0.7974 (t0) cc_final: 0.7753 (m-30)
REVERT: A  797 VAL cc_start: 0.8401 (m) cc_final: 0.7895 (t)
REVERT: A  911 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7387 (tttp)
REVERT: A  915 MET cc_start: 0.8269 (mpp) cc_final: 0.7643 (mpp)
REVERT: A 1006 ARG cc_start: 0.7617 (ttt90) cc_final: 0.7288 (ttt90)
REVERT: A 1062 LEU cc_start: 0.9378 (tp) cc_final: 0.9149 (tp)
REVERT: A 1111 ILE cc_start: 0.9387 (tt) cc_final: 0.9168 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 224
  average time/residue: 0.1961
  time to fit residues: 63.1188
Evaluate side-chains
  190 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 112 optimal weight:    0.9980
   chunk 58 optimal weight:   20.0000
   chunk 41 optimal weight:   30.0000
   chunk 62 optimal weight:    0.5980
   chunk 111 optimal weight:    8.9990
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:   20.0000
   chunk 2 optimal weight:    4.9990
   chunk 103 optimal weight:   20.0000
   chunk 56 optimal weight:   30.0000
   chunk 17 optimal weight:    0.0980
   overall best weight:    2.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 452 GLN
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 878 GLN
** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.164792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.121207 restraints weight = 19204.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.124740 restraints weight = 13143.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.127401 restraints weight = 9922.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9214  Z= 0.298
  Angle     :  0.675   9.874  12461  Z= 0.368
  Chirality :  0.043   0.251   1426
  Planarity :  0.004   0.056   1586
  Dihedral  : 11.653  99.948   1289
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  5.28 %
    Favored  : 94.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.44 (0.25), residues: 1153
  helix:  0.63 (0.19), residues: 719
  sheet:  0.07 (0.86), residues: 35
  loop : -2.02 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 694 
 HIS   0.004   0.001   HIS A 141 
 PHE   0.026   0.003   PHE A  71 
 TYR   0.016   0.002   TYR A 306 
 ARG   0.005   0.001   ARG A 534 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 222
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.7782 (ttm) cc_final: 0.7493 (tpt)
REVERT: A  107 MET cc_start: 0.8222 (mmm) cc_final: 0.7978 (mmm)
REVERT: A  174 ASP cc_start: 0.8260 (m-30) cc_final: 0.7887 (m-30)
REVERT: A  191 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8594 (tm-30)
REVERT: A  197 PHE cc_start: 0.8385 (m-80) cc_final: 0.8145 (m-80)
REVERT: A  295 MET cc_start: 0.7886 (ttt) cc_final: 0.7588 (ttt)
REVERT: A  436 MET cc_start: 0.9396 (mmp) cc_final: 0.9078 (mmm)
REVERT: A  465 ILE cc_start: 0.8602 (pt) cc_final: 0.8356 (mm)
REVERT: A  485 ARG cc_start: 0.7959 (mtm110) cc_final: 0.7664 (mtm110)
REVERT: A  508 PHE cc_start: 0.6276 (m-10) cc_final: 0.6062 (m-10)
REVERT: A  533 GLN cc_start: 0.8664 (pt0) cc_final: 0.8142 (tm-30)
REVERT: A  720 LEU cc_start: 0.9527 (mm) cc_final: 0.9278 (mm)
REVERT: A  765 THR cc_start: 0.8959 (m) cc_final: 0.8730 (m)
REVERT: A  796 ASP cc_start: 0.8261 (t0) cc_final: 0.7862 (m-30)
REVERT: A  821 VAL cc_start: 0.8199 (t) cc_final: 0.7759 (m)
REVERT: A  915 MET cc_start: 0.8426 (mpp) cc_final: 0.7856 (mpp)
REVERT: A 1006 ARG cc_start: 0.7567 (ttt90) cc_final: 0.7141 (ttt90)
  outliers start: 1
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1961
  time to fit residues: 61.3279
Evaluate side-chains
  190 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 48 optimal weight:    0.0670
   chunk 98 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 111 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 38 optimal weight:   20.0000
   chunk 46 optimal weight:    9.9990
   chunk 82 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 104 optimal weight:    6.9990
   overall best weight:    1.6124

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 805 ASN
A 878 GLN
** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.170015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.132242 restraints weight = 17888.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.133807 restraints weight = 12366.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.134360 restraints weight = 9222.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9214  Z= 0.215
  Angle     :  0.632   7.825  12461  Z= 0.336
  Chirality :  0.042   0.204   1426
  Planarity :  0.004   0.067   1586
  Dihedral  : 10.816 101.274   1289
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.38 %
    Favored  : 96.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.16 (0.25), residues: 1153
  helix:  0.87 (0.19), residues: 720
  sheet:  0.16 (0.87), residues: 35
  loop : -1.98 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 158 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.025   0.002   PHE A 755 
 TYR   0.015   0.002   TYR A 243 
 ARG   0.003   0.000   ARG A 485 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 227
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.7939 (ttm) cc_final: 0.7607 (tpt)
REVERT: A  103 LEU cc_start: 0.8829 (tp) cc_final: 0.8471 (tp)
REVERT: A  174 ASP cc_start: 0.8239 (m-30) cc_final: 0.7750 (m-30)
REVERT: A  436 MET cc_start: 0.9389 (mmp) cc_final: 0.9065 (mmm)
REVERT: A  465 ILE cc_start: 0.8624 (pt) cc_final: 0.8372 (mm)
REVERT: A  470 SER cc_start: 0.7876 (m) cc_final: 0.7159 (p)
REVERT: A  533 GLN cc_start: 0.8618 (pt0) cc_final: 0.8147 (tm-30)
REVERT: A  720 LEU cc_start: 0.9530 (mm) cc_final: 0.9296 (mm)
REVERT: A  765 THR cc_start: 0.8820 (m) cc_final: 0.8591 (m)
REVERT: A  796 ASP cc_start: 0.8205 (t0) cc_final: 0.7903 (m-30)
REVERT: A  813 ARG cc_start: 0.7840 (ttm170) cc_final: 0.7638 (ttm170)
REVERT: A  821 VAL cc_start: 0.8218 (t) cc_final: 0.7716 (m)
REVERT: A  871 GLU cc_start: 0.8258 (tt0) cc_final: 0.7831 (tt0)
REVERT: A  900 PHE cc_start: 0.9218 (t80) cc_final: 0.8692 (t80)
REVERT: A  915 MET cc_start: 0.8287 (mpp) cc_final: 0.7393 (mpp)
REVERT: A  937 THR cc_start: 0.9306 (t) cc_final: 0.8926 (t)
REVERT: A  945 MET cc_start: 0.7736 (ttt) cc_final: 0.7235 (ttt)
REVERT: A 1006 ARG cc_start: 0.7609 (ttt90) cc_final: 0.7203 (ttt90)
REVERT: A 1172 LEU cc_start: 0.7854 (tp) cc_final: 0.7649 (tp)
REVERT: A 1209 VAL cc_start: 0.9137 (t) cc_final: 0.8908 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 228
  average time/residue: 0.1934
  time to fit residues: 63.2369
Evaluate side-chains
  196 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 94 optimal weight:    0.1980
   chunk 110 optimal weight:   10.0000
   chunk 87 optimal weight:    0.9980
   chunk 6 optimal weight:    0.2980
   chunk 25 optimal weight:    6.9990
   chunk 109 optimal weight:   20.0000
   chunk 97 optimal weight:    2.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 367 ASN
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 878 GLN
** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.168480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.126906 restraints weight = 18012.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.130293 restraints weight = 12564.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.132682 restraints weight = 9506.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9214  Z= 0.213
  Angle     :  0.627   7.731  12461  Z= 0.333
  Chirality :  0.042   0.190   1426
  Planarity :  0.004   0.067   1586
  Dihedral  : 10.428 100.492   1289
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.32 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.08 (0.25), residues: 1153
  helix:  0.96 (0.19), residues: 720
  sheet:  0.10 (0.85), residues: 35
  loop : -1.97 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 704 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.029   0.002   PHE A 755 
 TYR   0.019   0.002   TYR A 306 
 ARG   0.006   0.000   ARG A 485 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 226
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LEU cc_start: 0.8806 (tp) cc_final: 0.8237 (tp)
REVERT: A  107 MET cc_start: 0.8568 (mmp) cc_final: 0.8346 (mmp)
REVERT: A  174 ASP cc_start: 0.8265 (m-30) cc_final: 0.7789 (m-30)
REVERT: A  259 THR cc_start: 0.9587 (p) cc_final: 0.9084 (p)
REVERT: A  263 PHE cc_start: 0.8458 (m-80) cc_final: 0.7850 (m-80)
REVERT: A  276 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8253 (t0)
REVERT: A  285 ILE cc_start: 0.9089 (mt) cc_final: 0.8886 (mt)
REVERT: A  306 TYR cc_start: 0.8274 (t80) cc_final: 0.7955 (t80)
REVERT: A  436 MET cc_start: 0.9368 (mmp) cc_final: 0.9055 (mmm)
REVERT: A  465 ILE cc_start: 0.8591 (pt) cc_final: 0.8331 (mm)
REVERT: A  470 SER cc_start: 0.7884 (m) cc_final: 0.7151 (p)
REVERT: A  485 ARG cc_start: 0.8087 (mtm110) cc_final: 0.7795 (mtm110)
REVERT: A  533 GLN cc_start: 0.8602 (pt0) cc_final: 0.8123 (tm-30)
REVERT: A  720 LEU cc_start: 0.9536 (mm) cc_final: 0.9255 (mm)
REVERT: A  765 THR cc_start: 0.8816 (m) cc_final: 0.8582 (m)
REVERT: A  785 ARG cc_start: 0.8470 (mtt180) cc_final: 0.7707 (ttm-80)
REVERT: A  796 ASP cc_start: 0.8252 (t0) cc_final: 0.7934 (m-30)
REVERT: A  821 VAL cc_start: 0.8230 (t) cc_final: 0.7702 (m)
REVERT: A  871 GLU cc_start: 0.8276 (tt0) cc_final: 0.7699 (tt0)
REVERT: A  900 PHE cc_start: 0.9255 (t80) cc_final: 0.8448 (t80)
REVERT: A  915 MET cc_start: 0.8285 (mpp) cc_final: 0.7651 (mpp)
REVERT: A  945 MET cc_start: 0.7562 (ttt) cc_final: 0.6907 (tmm)
REVERT: A 1006 ARG cc_start: 0.7554 (ttt90) cc_final: 0.7142 (ttt90)
REVERT: A 1111 ILE cc_start: 0.9423 (tt) cc_final: 0.9218 (tt)
REVERT: A 1172 LEU cc_start: 0.7619 (tp) cc_final: 0.7417 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 227
  average time/residue: 0.1802
  time to fit residues: 58.7824
Evaluate side-chains
  196 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 99 optimal weight:   20.0000
   chunk 91 optimal weight:    4.9990
   chunk 57 optimal weight:    9.9990
   chunk 111 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 59 optimal weight:    0.2980
   chunk 102 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
A 795 GLN
A 878 GLN
** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.171033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.130467 restraints weight = 17216.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.133499 restraints weight = 12340.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.135849 restraints weight = 9510.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9214  Z= 0.201
  Angle     :  0.620   8.103  12461  Z= 0.328
  Chirality :  0.042   0.182   1426
  Planarity :  0.004   0.067   1586
  Dihedral  : 10.167 101.804   1289
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.03 (0.25), residues: 1153
  helix:  1.07 (0.19), residues: 721
  sheet:  0.04 (0.84), residues: 35
  loop : -2.00 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP A 704 
 HIS   0.002   0.001   HIS A1003 
 PHE   0.023   0.002   PHE A 196 
 TYR   0.016   0.002   TYR A 440 
 ARG   0.005   0.000   ARG A 485 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 THR cc_start: 0.9517 (p) cc_final: 0.9301 (t)
REVERT: A  103 LEU cc_start: 0.8774 (tp) cc_final: 0.8344 (tp)
REVERT: A  174 ASP cc_start: 0.8172 (m-30) cc_final: 0.7742 (m-30)
REVERT: A  263 PHE cc_start: 0.8491 (m-80) cc_final: 0.7826 (m-80)
REVERT: A  281 LYS cc_start: 0.8656 (ptmm) cc_final: 0.7780 (ptmm)
REVERT: A  285 ILE cc_start: 0.9045 (mt) cc_final: 0.8826 (mt)
REVERT: A  436 MET cc_start: 0.9358 (mmp) cc_final: 0.9066 (mmm)
REVERT: A  465 ILE cc_start: 0.8579 (pt) cc_final: 0.8322 (mm)
REVERT: A  470 SER cc_start: 0.7858 (m) cc_final: 0.7048 (p)
REVERT: A  485 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7703 (mtm110)
REVERT: A  508 PHE cc_start: 0.6257 (m-10) cc_final: 0.6023 (m-10)
REVERT: A  533 GLN cc_start: 0.8577 (pt0) cc_final: 0.8266 (tp-100)
REVERT: A  765 THR cc_start: 0.8758 (m) cc_final: 0.8554 (m)
REVERT: A  796 ASP cc_start: 0.8188 (t0) cc_final: 0.7894 (m-30)
REVERT: A  821 VAL cc_start: 0.8318 (t) cc_final: 0.7824 (m)
REVERT: A  871 GLU cc_start: 0.8285 (tt0) cc_final: 0.7658 (tt0)
REVERT: A  900 PHE cc_start: 0.9121 (t80) cc_final: 0.8703 (t80)
REVERT: A  915 MET cc_start: 0.8265 (mpp) cc_final: 0.7350 (mpp)
REVERT: A  937 THR cc_start: 0.9270 (t) cc_final: 0.8820 (t)
REVERT: A  945 MET cc_start: 0.7339 (ttt) cc_final: 0.6566 (tmm)
REVERT: A 1006 ARG cc_start: 0.7509 (ttt90) cc_final: 0.7031 (ttt90)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.1915
  time to fit residues: 60.4415
Evaluate side-chains
  189 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 95 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 101 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 99 optimal weight:    6.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
A 834 GLN
A 878 GLN
A 932 HIS
** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.162450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.120302 restraints weight = 18372.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.123507 restraints weight = 12910.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.125628 restraints weight = 9843.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   9214  Z= 0.347
  Angle     :  0.729   8.821  12461  Z= 0.401
  Chirality :  0.047   0.380   1426
  Planarity :  0.005   0.064   1586
  Dihedral  : 10.566 102.450   1289
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 15.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.90 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.58 (0.25), residues: 1153
  helix:  0.49 (0.19), residues: 726
  sheet: -0.27 (0.82), residues: 35
  loop : -2.04 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP A 704 
 HIS   0.005   0.001   HIS A 149 
 PHE   0.042   0.003   PHE A  71 
 TYR   0.027   0.003   TYR A 306 
 ARG   0.006   0.001   ARG A1134 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 219
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.7953 (tpt) cc_final: 0.7551 (tpt)
REVERT: A  103 LEU cc_start: 0.8961 (tp) cc_final: 0.8468 (tp)
REVERT: A  174 ASP cc_start: 0.8362 (m-30) cc_final: 0.7937 (m-30)
REVERT: A  263 PHE cc_start: 0.8372 (m-80) cc_final: 0.7854 (m-80)
REVERT: A  281 LYS cc_start: 0.8747 (ptmm) cc_final: 0.7941 (ptmm)
REVERT: A  285 ILE cc_start: 0.9224 (mt) cc_final: 0.9021 (mt)
REVERT: A  306 TYR cc_start: 0.8287 (t80) cc_final: 0.7769 (t80)
REVERT: A  436 MET cc_start: 0.9405 (mmp) cc_final: 0.9087 (mmm)
REVERT: A  470 SER cc_start: 0.7910 (m) cc_final: 0.7078 (p)
REVERT: A  533 GLN cc_start: 0.8610 (pt0) cc_final: 0.8183 (tm-30)
REVERT: A  584 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7780 (ttp80)
REVERT: A  720 LEU cc_start: 0.9556 (mm) cc_final: 0.9325 (mm)
REVERT: A  796 ASP cc_start: 0.8326 (t0) cc_final: 0.8055 (m-30)
REVERT: A  821 VAL cc_start: 0.8364 (t) cc_final: 0.7853 (m)
REVERT: A  871 GLU cc_start: 0.8446 (tt0) cc_final: 0.7944 (tt0)
REVERT: A  900 PHE cc_start: 0.9140 (t80) cc_final: 0.8567 (t80)
REVERT: A  937 THR cc_start: 0.9375 (t) cc_final: 0.9040 (t)
REVERT: A  945 MET cc_start: 0.7493 (ttt) cc_final: 0.6661 (tmm)
REVERT: A 1006 ARG cc_start: 0.7444 (ttt90) cc_final: 0.6852 (ttt90)
REVERT: A 1172 LEU cc_start: 0.7665 (tp) cc_final: 0.7425 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 220
  average time/residue: 0.2120
  time to fit residues: 65.8944
Evaluate side-chains
  176 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 94 optimal weight:    7.9990
   chunk 96 optimal weight:   20.0000
   chunk 105 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 878 GLN
** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.165936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.129765 restraints weight = 17169.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.131737 restraints weight = 11711.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.132812 restraints weight = 8187.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9214  Z= 0.271
  Angle     :  0.674   7.986  12461  Z= 0.364
  Chirality :  0.044   0.325   1426
  Planarity :  0.004   0.066   1586
  Dihedral  : 10.584 105.791   1289
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.49 (0.25), residues: 1153
  helix:  0.63 (0.19), residues: 720
  sheet: -0.25 (0.83), residues: 35
  loop : -2.12 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 704 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.025   0.002   PHE A 196 
 TYR   0.017   0.002   TYR A 113 
 ARG   0.008   0.000   ARG A 485 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.7634 (tpt) cc_final: 0.7366 (tpt)
REVERT: A  103 LEU cc_start: 0.8948 (tp) cc_final: 0.8516 (tp)
REVERT: A  174 ASP cc_start: 0.8230 (m-30) cc_final: 0.7871 (m-30)
REVERT: A  263 PHE cc_start: 0.8337 (m-80) cc_final: 0.7832 (m-80)
REVERT: A  281 LYS cc_start: 0.8761 (ptmm) cc_final: 0.7915 (ptmm)
REVERT: A  285 ILE cc_start: 0.9256 (mt) cc_final: 0.9045 (mt)
REVERT: A  306 TYR cc_start: 0.8099 (t80) cc_final: 0.7853 (t80)
REVERT: A  436 MET cc_start: 0.9336 (mmp) cc_final: 0.9080 (mmm)
REVERT: A  470 SER cc_start: 0.7911 (m) cc_final: 0.7085 (p)
REVERT: A  485 ARG cc_start: 0.8145 (mtm110) cc_final: 0.7901 (mtm110)
REVERT: A  533 GLN cc_start: 0.8551 (pt0) cc_final: 0.8124 (tm-30)
REVERT: A  796 ASP cc_start: 0.8199 (t0) cc_final: 0.7962 (m-30)
REVERT: A  821 VAL cc_start: 0.8371 (t) cc_final: 0.7823 (m)
REVERT: A  871 GLU cc_start: 0.8378 (tt0) cc_final: 0.7539 (tt0)
REVERT: A  900 PHE cc_start: 0.9108 (t80) cc_final: 0.8486 (t80)
REVERT: A  937 THR cc_start: 0.9222 (t) cc_final: 0.8568 (t)
REVERT: A  945 MET cc_start: 0.7376 (ttt) cc_final: 0.6427 (tmm)
REVERT: A 1006 ARG cc_start: 0.7396 (ttt90) cc_final: 0.6732 (ttt90)
REVERT: A 1172 LEU cc_start: 0.7678 (tp) cc_final: 0.7448 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1903
  time to fit residues: 55.9183
Evaluate side-chains
  175 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 41 optimal weight:   20.0000
   chunk 64 optimal weight:    0.7980
   chunk 99 optimal weight:    7.9990
   chunk 3 optimal weight:    0.6980
   chunk 94 optimal weight:    1.9990
   chunk 112 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 70 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 109 optimal weight:   20.0000
   chunk 58 optimal weight:    5.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
A 878 GLN
** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.166929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.128715 restraints weight = 17219.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.130998 restraints weight = 12941.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.132852 restraints weight = 10358.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9214  Z= 0.252
  Angle     :  0.680   8.371  12461  Z= 0.367
  Chirality :  0.044   0.319   1426
  Planarity :  0.004   0.067   1586
  Dihedral  : 10.327  98.778   1289
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.46 (0.25), residues: 1153
  helix:  0.68 (0.19), residues: 720
  sheet: -0.26 (0.83), residues: 35
  loop : -2.16 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 704 
 HIS   0.003   0.001   HIS A1003 
 PHE   0.025   0.002   PHE A 196 
 TYR   0.024   0.002   TYR A 114 
 ARG   0.008   0.000   ARG A 485 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.7227 (tpt) cc_final: 0.7003 (tpt)
REVERT: A  103 LEU cc_start: 0.8899 (tp) cc_final: 0.8560 (tp)
REVERT: A  174 ASP cc_start: 0.8126 (m-30) cc_final: 0.7839 (m-30)
REVERT: A  263 PHE cc_start: 0.8291 (m-80) cc_final: 0.7667 (m-80)
REVERT: A  281 LYS cc_start: 0.8722 (ptmm) cc_final: 0.7874 (ptmm)
REVERT: A  285 ILE cc_start: 0.9290 (mt) cc_final: 0.9084 (mt)
REVERT: A  306 TYR cc_start: 0.8127 (t80) cc_final: 0.7681 (t80)
REVERT: A  436 MET cc_start: 0.9279 (mmp) cc_final: 0.9069 (mmm)
REVERT: A  470 SER cc_start: 0.7924 (m) cc_final: 0.7145 (p)
REVERT: A  485 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7785 (mtm110)
REVERT: A  533 GLN cc_start: 0.8450 (pt0) cc_final: 0.8076 (tm-30)
REVERT: A  584 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7673 (ttp80)
REVERT: A  821 VAL cc_start: 0.8435 (t) cc_final: 0.7868 (m)
REVERT: A  871 GLU cc_start: 0.8384 (tt0) cc_final: 0.7526 (tt0)
REVERT: A  900 PHE cc_start: 0.9155 (t80) cc_final: 0.8516 (t80)
REVERT: A  937 THR cc_start: 0.9120 (t) cc_final: 0.8378 (t)
REVERT: A  945 MET cc_start: 0.7435 (ttt) cc_final: 0.6392 (tmm)
REVERT: A  968 GLU cc_start: 0.7689 (pp20) cc_final: 0.7467 (pp20)
REVERT: A 1006 ARG cc_start: 0.7296 (ttt90) cc_final: 0.6607 (ttt90)
REVERT: A 1178 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8480 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2080
  time to fit residues: 62.5207
Evaluate side-chains
  182 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 41 optimal weight:   20.0000
   chunk 1 optimal weight:    0.9990
   chunk 114 optimal weight:   30.0000
   chunk 95 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 878 GLN
** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.170220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.131549 restraints weight = 16633.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.134360 restraints weight = 11901.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.136660 restraints weight = 9167.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9214  Z= 0.190
  Angle     :  0.652   8.440  12461  Z= 0.346
  Chirality :  0.044   0.296   1426
  Planarity :  0.004   0.070   1586
  Dihedral  : 10.035  99.856   1289
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.17 (0.25), residues: 1153
  helix:  0.95 (0.19), residues: 720
  sheet: -0.09 (0.85), residues: 35
  loop : -2.13 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP A 694 
 HIS   0.004   0.001   HIS A1003 
 PHE   0.023   0.002   PHE A 767 
 TYR   0.019   0.002   TYR A 949 
 ARG   0.008   0.001   ARG A 485 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3029.05 seconds
wall clock time: 55 minutes 8.83 seconds (3308.83 seconds total)