Starting phenix.real_space_refine
on Tue Mar  3 22:49:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zkb_14761/03_2026/7zkb_14761.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zkb_14761/03_2026/7zkb_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zkb_14761/03_2026/7zkb_14761.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zkb_14761/03_2026/7zkb_14761.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zkb_14761/03_2026/7zkb_14761.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zkb_14761/03_2026/7zkb_14761.map"
  }
  resolution = 4.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.08, per 1000 atoms: 0.23
  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: 0.83
  Conformation dependent library (CDL) restraints added in 409.6 milliseconds
  

  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: 0.31
  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: 1.46

  Time building geometry restraints manager: 1.05 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:             1.460
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.510
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.570
-------------------------------------------------------------------------------
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   9215  Z= 0.457
  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 : 16.27
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.26), 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
 ARG   0.006   0.000   ARG A1134 
 TYR   0.017   0.002   TYR A 113 
 PHE   0.016   0.001   PHE A1038 
 TRP   0.017   0.001   TRP A 704 
 HIS   0.004   0.000   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00773 ( 9214)
  covalent geometry    : angle       1.04511 (12461)
  hydrogen bonds       : bond        0.12531 (  559)
  hydrogen bonds       : angle       5.76747 ( 1668)
  Misc. bond           : bond        0.02896 (    1)

*********************** 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  : 0.218 
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: 0.7521 (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: 0.8570 (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: 0.9076 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 246
  average time/residue: 0.0764
  time to fit residues: 27.0103
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  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.0770
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0670
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.5276

-------------------------------------------------------------------------------
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 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
A 583 HIS
A 737 ASN
A 795 GLN
A 878 GLN
A1103 GLN
A1253 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.176179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.133825 restraints weight = 18757.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.137045 restraints weight = 13353.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.139473 restraints weight = 10269.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.141311 restraints weight = 8355.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.142448 restraints weight = 7125.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9215  Z= 0.135
  Angle     :  0.606   7.514  12461  Z= 0.318
  Chirality :  0.041   0.200   1426
  Planarity :  0.004   0.067   1586
  Dihedral  : 12.488 109.094   1289
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  3.38 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.26), residues: 1153
  helix:  1.15 (0.20), residues: 713
  sheet:  0.41 (0.85), residues: 35
  loop : -1.76 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 485 
 TYR   0.017   0.002   TYR A 243 
 PHE   0.039   0.002   PHE A 755 
 TRP   0.018   0.001   TRP A 704 
 HIS   0.003   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9214)
  covalent geometry    : angle       0.60557 (12461)
  hydrogen bonds       : bond        0.04976 (  559)
  hydrogen bonds       : angle       4.53171 ( 1668)
  Misc. bond           : bond        0.00012 (    1)

*********************** 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
  244 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 241
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 MET cc_start: 0.7684 (tpp) cc_final: 0.7479 (mmt)
REVERT: A  107 MET cc_start: 0.8140 (mmm) cc_final: 0.7920 (mmm)
REVERT: A  259 THR cc_start: 0.9650 (p) cc_final: 0.9365 (p)
REVERT: A  263 PHE cc_start: 0.8605 (m-80) cc_final: 0.8167 (m-80)
REVERT: A  295 MET cc_start: 0.7850 (ttt) cc_final: 0.7144 (ttt)
REVERT: A  436 MET cc_start: 0.9323 (mmp) cc_final: 0.9020 (mmm)
REVERT: A  720 LEU cc_start: 0.9402 (mm) cc_final: 0.9173 (mm)
REVERT: A  765 THR cc_start: 0.8886 (m) cc_final: 0.8665 (m)
REVERT: A  785 ARG cc_start: 0.8134 (mtt180) cc_final: 0.7743 (ttm-80)
REVERT: A  813 ARG cc_start: 0.8020 (tpt170) cc_final: 0.7820 (ttm170)
REVERT: A  915 MET cc_start: 0.7862 (mpp) cc_final: 0.7448 (mpp)
REVERT: A  966 THR cc_start: 0.7950 (p) cc_final: 0.7687 (p)
REVERT: A 1006 ARG cc_start: 0.7564 (ttt90) cc_final: 0.7238 (ttt90)
REVERT: A 1020 GLN cc_start: 0.8110 (pp30) cc_final: 0.7825 (pp30)
REVERT: A 1062 LEU cc_start: 0.9338 (tp) cc_final: 0.9111 (tp)
REVERT: A 1084 ASP cc_start: 0.8659 (p0) cc_final: 0.7500 (t0)
REVERT: A 1121 ARG cc_start: 0.5772 (tpt170) cc_final: 0.5570 (tpt-90)
REVERT: A 1209 VAL cc_start: 0.9122 (t) cc_final: 0.8869 (p)
REVERT: A 1211 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8835 (pp30)
  outliers start: 3
  outliers final: 0
  residues processed: 242
  average time/residue: 0.0790
  time to fit residues: 27.5800
Evaluate side-chains
  202 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 201
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 52 optimal weight:   20.0000
   chunk 107 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 88 optimal weight:    0.2980
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
A 795 GLN
A 878 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.176088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.136614 restraints weight = 18188.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.138102 restraints weight = 12721.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.138927 restraints weight = 10130.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.139397 restraints weight = 8816.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.139681 restraints weight = 8237.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9215  Z= 0.131
  Angle     :  0.592   7.795  12461  Z= 0.312
  Chirality :  0.041   0.168   1426
  Planarity :  0.004   0.062   1586
  Dihedral  : 11.833 107.738   1289
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.80 %
    Favored  : 96.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.25), residues: 1153
  helix:  1.14 (0.20), residues: 719
  sheet:  0.32 (0.84), residues: 35
  loop : -1.78 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 460 
 TYR   0.015   0.001   TYR A 243 
 PHE   0.018   0.002   PHE A 331 
 TRP   0.015   0.001   TRP A 799 
 HIS   0.010   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9214)
  covalent geometry    : angle       0.59203 (12461)
  hydrogen bonds       : bond        0.04577 (  559)
  hydrogen bonds       : angle       4.46531 ( 1668)
  Misc. bond           : bond        0.01071 (    1)

*********************** 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
  229 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 228
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7975 (tpp) cc_final: 0.7501 (mmm)
REVERT: A  174 ASP cc_start: 0.8008 (m-30) cc_final: 0.7650 (m-30)
REVERT: A  259 THR cc_start: 0.9642 (p) cc_final: 0.9330 (p)
REVERT: A  295 MET cc_start: 0.7840 (ttt) cc_final: 0.7185 (ttm)
REVERT: A  436 MET cc_start: 0.9354 (mmp) cc_final: 0.9026 (mmm)
REVERT: A  465 ILE cc_start: 0.8597 (pt) cc_final: 0.8268 (mm)
REVERT: A  485 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7737 (mtm110)
REVERT: A  704 TRP cc_start: 0.7246 (p-90) cc_final: 0.6967 (p-90)
REVERT: A  720 LEU cc_start: 0.9434 (mm) cc_final: 0.9223 (mm)
REVERT: A  765 THR cc_start: 0.8855 (m) cc_final: 0.8635 (m)
REVERT: A  785 ARG cc_start: 0.8055 (mtt180) cc_final: 0.6810 (ttm-80)
REVERT: A  814 LEU cc_start: 0.8590 (mt) cc_final: 0.8203 (mt)
REVERT: A  915 MET cc_start: 0.8036 (mpp) cc_final: 0.7566 (mpp)
REVERT: A 1006 ARG cc_start: 0.7659 (ttt90) cc_final: 0.7342 (ttt90)
REVERT: A 1062 LEU cc_start: 0.9341 (tp) cc_final: 0.9097 (tp)
REVERT: A 1084 ASP cc_start: 0.8633 (p0) cc_final: 0.7477 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 228
  average time/residue: 0.0822
  time to fit residues: 26.9263
Evaluate side-chains
  199 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 104 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0670
   chunk 26 optimal weight:    4.9990
   chunk 112 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0980
   chunk 74 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 105 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    1.2122

-------------------------------------------------------------------------------
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 394 HIS
A 452 GLN
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
A 878 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.173546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.130939 restraints weight = 18245.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.134253 restraints weight = 12834.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.136749 restraints weight = 9763.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.138552 restraints weight = 7895.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.139726 restraints weight = 6714.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9215  Z= 0.140
  Angle     :  0.595   7.821  12461  Z= 0.316
  Chirality :  0.041   0.272   1426
  Planarity :  0.004   0.067   1586
  Dihedral  : 11.334 105.578   1289
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.12 %
    Favored  : 95.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.25), residues: 1153
  helix:  1.19 (0.20), residues: 719
  sheet:  0.40 (0.85), residues: 35
  loop : -1.81 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 534 
 TYR   0.036   0.002   TYR A 114 
 PHE   0.027   0.002   PHE A  78 
 TRP   0.009   0.001   TRP A 311 
 HIS   0.002   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9214)
  covalent geometry    : angle       0.59482 (12461)
  hydrogen bonds       : bond        0.04479 (  559)
  hydrogen bonds       : angle       4.41392 ( 1668)
  Misc. bond           : bond        0.00004 (    1)

*********************** 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
  229 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 228
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.8154 (tpp) cc_final: 0.7433 (mmm)
REVERT: A  174 ASP cc_start: 0.7958 (m-30) cc_final: 0.7592 (m-30)
REVERT: A  263 PHE cc_start: 0.8367 (m-80) cc_final: 0.7713 (m-80)
REVERT: A  295 MET cc_start: 0.7825 (ttt) cc_final: 0.7147 (ttm)
REVERT: A  334 VAL cc_start: 0.9047 (t) cc_final: 0.8642 (m)
REVERT: A  436 MET cc_start: 0.9301 (mmp) cc_final: 0.8992 (mmm)
REVERT: A  465 ILE cc_start: 0.8578 (pt) cc_final: 0.8261 (mm)
REVERT: A  704 TRP cc_start: 0.7289 (p-90) cc_final: 0.7023 (p-90)
REVERT: A  720 LEU cc_start: 0.9439 (mm) cc_final: 0.9213 (mm)
REVERT: A  765 THR cc_start: 0.8865 (m) cc_final: 0.8633 (m)
REVERT: A  785 ARG cc_start: 0.8168 (mtt180) cc_final: 0.6937 (ttm-80)
REVERT: A  814 LEU cc_start: 0.8674 (mt) cc_final: 0.8274 (mt)
REVERT: A  915 MET cc_start: 0.8031 (mpp) cc_final: 0.7405 (mpp)
REVERT: A 1006 ARG cc_start: 0.7522 (ttt90) cc_final: 0.7229 (ttt90)
REVERT: A 1060 GLN cc_start: 0.6533 (tp-100) cc_final: 0.5907 (tp-100)
REVERT: A 1062 LEU cc_start: 0.9337 (tp) cc_final: 0.8569 (tp)
REVERT: A 1084 ASP cc_start: 0.8607 (p0) cc_final: 0.8316 (p0)
REVERT: A 1178 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8261 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 228
  average time/residue: 0.0779
  time to fit residues: 25.5794
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  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 39 optimal weight:    0.3980
   chunk 7 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 88 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0010
   chunk 48 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    0.6388

-------------------------------------------------------------------------------
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 394 HIS
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
A 737 ASN
A 878 GLN
** A1020 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 = 0.4126 r_free = 0.4126 target = 0.176616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.137626 restraints weight = 18614.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.141140 restraints weight = 13050.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.140734 restraints weight = 8902.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.141348 restraints weight = 8759.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.141655 restraints weight = 8335.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9215  Z= 0.123
  Angle     :  0.593   8.084  12461  Z= 0.307
  Chirality :  0.041   0.214   1426
  Planarity :  0.004   0.067   1586
  Dihedral  : 10.924 104.472   1289
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.75 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.26), residues: 1153
  helix:  1.29 (0.20), residues: 720
  sheet:  0.47 (0.84), residues: 35
  loop : -1.84 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 485 
 TYR   0.016   0.001   TYR A 397 
 PHE   0.033   0.002   PHE A  78 
 TRP   0.008   0.001   TRP A 311 
 HIS   0.003   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9214)
  covalent geometry    : angle       0.59293 (12461)
  hydrogen bonds       : bond        0.04299 (  559)
  hydrogen bonds       : angle       4.30303 ( 1668)
  Misc. bond           : bond        0.00041 (    1)

*********************** 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
  232 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 231
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ILE cc_start: 0.8806 (mt) cc_final: 0.8583 (mt)
REVERT: A  152 MET cc_start: 0.8172 (tpp) cc_final: 0.7247 (mmm)
REVERT: A  174 ASP cc_start: 0.8023 (m-30) cc_final: 0.7668 (m-30)
REVERT: A  259 THR cc_start: 0.9661 (p) cc_final: 0.9193 (p)
REVERT: A  263 PHE cc_start: 0.8370 (m-80) cc_final: 0.7829 (m-80)
REVERT: A  334 VAL cc_start: 0.9048 (t) cc_final: 0.8671 (m)
REVERT: A  436 MET cc_start: 0.9309 (mmp) cc_final: 0.8977 (mmm)
REVERT: A  465 ILE cc_start: 0.8592 (pt) cc_final: 0.8288 (mm)
REVERT: A  485 ARG cc_start: 0.8115 (mtm110) cc_final: 0.7772 (mtm110)
REVERT: A  765 THR cc_start: 0.8821 (m) cc_final: 0.8582 (m)
REVERT: A  785 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7986 (ttm110)
REVERT: A  911 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7369 (tttp)
REVERT: A  915 MET cc_start: 0.7932 (mpp) cc_final: 0.6979 (mpp)
REVERT: A 1006 ARG cc_start: 0.7615 (ttt90) cc_final: 0.7321 (ttt90)
REVERT: A 1060 GLN cc_start: 0.6516 (tp-100) cc_final: 0.5850 (tp-100)
  outliers start: 1
  outliers final: 0
  residues processed: 232
  average time/residue: 0.0751
  time to fit residues: 25.0853
Evaluate side-chains
  192 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 17 optimal weight:    0.4980
   chunk 16 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 92 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0970
   chunk 82 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   chunk 105 optimal weight:    0.7980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.174317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.131369 restraints weight = 18819.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.134414 restraints weight = 13760.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.136688 restraints weight = 10753.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.138349 restraints weight = 8864.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.139350 restraints weight = 7657.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9215  Z= 0.132
  Angle     :  0.605   8.009  12461  Z= 0.316
  Chirality :  0.041   0.193   1426
  Planarity :  0.004   0.065   1586
  Dihedral  : 10.605 102.076   1289
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.32 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.25), residues: 1153
  helix:  1.32 (0.20), residues: 714
  sheet:  0.25 (0.82), residues: 35
  loop : -1.91 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 485 
 TYR   0.016   0.001   TYR A 440 
 PHE   0.031   0.002   PHE A  78 
 TRP   0.009   0.001   TRP A 311 
 HIS   0.002   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9214)
  covalent geometry    : angle       0.60533 (12461)
  hydrogen bonds       : bond        0.04301 (  559)
  hydrogen bonds       : angle       4.34892 ( 1668)
  Misc. bond           : bond        0.00021 (    1)

*********************** 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
  227 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 226
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LEU cc_start: 0.8535 (tp) cc_final: 0.8167 (tp)
REVERT: A  152 MET cc_start: 0.8318 (tpp) cc_final: 0.7296 (mmm)
REVERT: A  174 ASP cc_start: 0.8044 (m-30) cc_final: 0.7695 (m-30)
REVERT: A  263 PHE cc_start: 0.8491 (m-80) cc_final: 0.7945 (m-80)
REVERT: A  281 LYS cc_start: 0.8267 (pttp) cc_final: 0.7260 (pttp)
REVERT: A  436 MET cc_start: 0.9359 (mmp) cc_final: 0.9002 (mmm)
REVERT: A  485 ARG cc_start: 0.7983 (mtm110) cc_final: 0.7618 (mtm110)
REVERT: A  704 TRP cc_start: 0.7475 (p-90) cc_final: 0.7202 (p-90)
REVERT: A  720 LEU cc_start: 0.9445 (mm) cc_final: 0.9229 (mm)
REVERT: A  765 THR cc_start: 0.8833 (m) cc_final: 0.8584 (m)
REVERT: A  785 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7204 (ttm-80)
REVERT: A  814 LEU cc_start: 0.8664 (mt) cc_final: 0.7887 (mt)
REVERT: A  911 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7352 (tttp)
REVERT: A  915 MET cc_start: 0.8062 (mpp) cc_final: 0.7312 (mpp)
REVERT: A 1006 ARG cc_start: 0.7590 (ttt90) cc_final: 0.7209 (ttt90)
REVERT: A 1178 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8393 (tm-30)
REVERT: A 1209 VAL cc_start: 0.9130 (t) cc_final: 0.8869 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 227
  average time/residue: 0.0768
  time to fit residues: 24.9070
Evaluate side-chains
  193 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 39 optimal weight:   20.0000
   chunk 21 optimal weight:   10.0000
   chunk 72 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   overall best weight:    2.1184

-------------------------------------------------------------------------------
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 805 ASN
A 878 GLN
A1020 GLN
** A1211 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 = 0.4038 r_free = 0.4038 target = 0.168810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.125509 restraints weight = 18118.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.128508 restraints weight = 13035.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.130801 restraints weight = 10120.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.132222 restraints weight = 8303.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.133595 restraints weight = 7206.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9215  Z= 0.184
  Angle     :  0.642   8.002  12461  Z= 0.343
  Chirality :  0.042   0.178   1426
  Planarity :  0.004   0.064   1586
  Dihedral  : 10.715  98.405   1289
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.69 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.25), residues: 1153
  helix:  1.10 (0.19), residues: 714
  sheet:  0.06 (0.81), residues: 35
  loop : -1.97 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 485 
 TYR   0.019   0.002   TYR A1017 
 PHE   0.025   0.002   PHE A  78 
 TRP   0.012   0.002   TRP A 694 
 HIS   0.003   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 9214)
  covalent geometry    : angle       0.64206 (12461)
  hydrogen bonds       : bond        0.04590 (  559)
  hydrogen bonds       : angle       4.53506 ( 1668)
  Misc. bond           : bond        0.00023 (    1)

*********************** 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
  226 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 225
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LEU cc_start: 0.8678 (tp) cc_final: 0.8372 (tp)
REVERT: A  154 GLN cc_start: 0.8983 (mt0) cc_final: 0.8740 (tt0)
REVERT: A  174 ASP cc_start: 0.8135 (m-30) cc_final: 0.7760 (m-30)
REVERT: A  263 PHE cc_start: 0.8519 (m-80) cc_final: 0.7932 (m-80)
REVERT: A  306 TYR cc_start: 0.8079 (t80) cc_final: 0.7874 (t80)
REVERT: A  436 MET cc_start: 0.9361 (mmp) cc_final: 0.8987 (mmm)
REVERT: A  533 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8475 (tm-30)
REVERT: A  720 LEU cc_start: 0.9526 (mm) cc_final: 0.9282 (mm)
REVERT: A  766 PHE cc_start: 0.8355 (m-80) cc_final: 0.8092 (m-80)
REVERT: A  785 ARG cc_start: 0.8497 (mtt180) cc_final: 0.7265 (ttm-80)
REVERT: A  797 VAL cc_start: 0.8852 (m) cc_final: 0.8022 (t)
REVERT: A  814 LEU cc_start: 0.8965 (mt) cc_final: 0.8042 (mt)
REVERT: A  821 VAL cc_start: 0.8218 (t) cc_final: 0.7681 (m)
REVERT: A  900 PHE cc_start: 0.9139 (t80) cc_final: 0.8881 (t80)
REVERT: A  915 MET cc_start: 0.8242 (mpp) cc_final: 0.7619 (mpp)
REVERT: A 1006 ARG cc_start: 0.7603 (ttt90) cc_final: 0.7109 (ttt90)
REVERT: A 1025 ASN cc_start: 0.7855 (m-40) cc_final: 0.7318 (p0)
REVERT: A 1207 GLU cc_start: 0.7640 (tp30) cc_final: 0.7363 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 226
  average time/residue: 0.0785
  time to fit residues: 25.4643
Evaluate side-chains
  186 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 107 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 86 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
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**
** A1211 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 = 0.4049 r_free = 0.4049 target = 0.169905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.130028 restraints weight = 18899.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.131195 restraints weight = 15993.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.131923 restraints weight = 11684.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.132968 restraints weight = 10176.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.133432 restraints weight = 9176.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9215  Z= 0.178
  Angle     :  0.651   7.964  12461  Z= 0.348
  Chirality :  0.043   0.176   1426
  Planarity :  0.004   0.068   1586
  Dihedral  : 10.757  97.835   1289
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.25), residues: 1153
  helix:  1.03 (0.19), residues: 720
  sheet: -0.13 (0.79), residues: 35
  loop : -1.93 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 485 
 TYR   0.020   0.002   TYR A1017 
 PHE   0.034   0.002   PHE A  78 
 TRP   0.012   0.001   TRP A  44 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 9214)
  covalent geometry    : angle       0.65112 (12461)
  hydrogen bonds       : bond        0.04654 (  559)
  hydrogen bonds       : angle       4.55306 ( 1668)
  Misc. bond           : bond        0.00013 (    1)

*********************** 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
  221 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LEU cc_start: 0.8738 (tp) cc_final: 0.8342 (tp)
REVERT: A  174 ASP cc_start: 0.8093 (m-30) cc_final: 0.7701 (m-30)
REVERT: A  197 PHE cc_start: 0.8419 (m-80) cc_final: 0.8083 (m-80)
REVERT: A  259 THR cc_start: 0.9653 (p) cc_final: 0.9235 (p)
REVERT: A  263 PHE cc_start: 0.8371 (m-80) cc_final: 0.7794 (m-80)
REVERT: A  436 MET cc_start: 0.9341 (mmp) cc_final: 0.8986 (mmm)
REVERT: A  485 ARG cc_start: 0.8205 (mtm110) cc_final: 0.8000 (mtm110)
REVERT: A  533 GLN cc_start: 0.8789 (tp-100) cc_final: 0.8402 (tm-30)
REVERT: A  785 ARG cc_start: 0.8530 (mtt180) cc_final: 0.7245 (ttm-80)
REVERT: A  814 LEU cc_start: 0.8973 (mt) cc_final: 0.7935 (mt)
REVERT: A  821 VAL cc_start: 0.8296 (t) cc_final: 0.7708 (m)
REVERT: A  900 PHE cc_start: 0.9261 (t80) cc_final: 0.8979 (t80)
REVERT: A  968 GLU cc_start: 0.7656 (pp20) cc_final: 0.7453 (pp20)
REVERT: A 1006 ARG cc_start: 0.7568 (ttt90) cc_final: 0.7063 (ttt90)
REVERT: A 1172 LEU cc_start: 0.7828 (tp) cc_final: 0.7611 (tp)
REVERT: A 1178 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8571 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0771
  time to fit residues: 24.6856
Evaluate side-chains
  194 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 89 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 100 optimal weight:    8.9990
   chunk 110 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   chunk 108 optimal weight:    5.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 168 ASN
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**
** A1211 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 = 0.4069 r_free = 0.4069 target = 0.171769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.132217 restraints weight = 18665.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.134338 restraints weight = 14113.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.134097 restraints weight = 10033.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.134880 restraints weight = 10098.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.135429 restraints weight = 9031.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9215  Z= 0.156
  Angle     :  0.642   8.145  12461  Z= 0.341
  Chirality :  0.043   0.365   1426
  Planarity :  0.004   0.065   1586
  Dihedral  : 10.633  97.576   1289
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.25), residues: 1153
  helix:  0.95 (0.19), residues: 728
  sheet: -0.12 (0.80), residues: 35
  loop : -2.01 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 485 
 TYR   0.018   0.002   TYR A 306 
 PHE   0.036   0.002   PHE A  78 
 TRP   0.049   0.002   TRP A 158 
 HIS   0.005   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9214)
  covalent geometry    : angle       0.64153 (12461)
  hydrogen bonds       : bond        0.04603 (  559)
  hydrogen bonds       : angle       4.52661 ( 1668)
  Misc. bond           : bond        0.00015 (    1)

*********************** 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
  220 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 THR cc_start: 0.9502 (p) cc_final: 0.9283 (t)
REVERT: A  103 LEU cc_start: 0.8769 (tp) cc_final: 0.8352 (tp)
REVERT: A  113 TYR cc_start: 0.7331 (t80) cc_final: 0.7128 (t80)
REVERT: A  174 ASP cc_start: 0.8049 (m-30) cc_final: 0.7688 (m-30)
REVERT: A  197 PHE cc_start: 0.8355 (m-80) cc_final: 0.8067 (m-80)
REVERT: A  259 THR cc_start: 0.9656 (p) cc_final: 0.9277 (p)
REVERT: A  263 PHE cc_start: 0.8393 (m-80) cc_final: 0.7840 (m-80)
REVERT: A  364 ILE cc_start: 0.8716 (mp) cc_final: 0.8315 (tp)
REVERT: A  436 MET cc_start: 0.9364 (mmp) cc_final: 0.8990 (mmm)
REVERT: A  485 ARG cc_start: 0.8109 (mtm110) cc_final: 0.7838 (mtm110)
REVERT: A  765 THR cc_start: 0.8826 (m) cc_final: 0.8612 (m)
REVERT: A  821 VAL cc_start: 0.8258 (t) cc_final: 0.7698 (m)
REVERT: A  900 PHE cc_start: 0.9314 (t80) cc_final: 0.8971 (t80)
REVERT: A 1006 ARG cc_start: 0.7585 (ttt90) cc_final: 0.7094 (ttt90)
REVERT: A 1010 LYS cc_start: 0.8515 (tmtt) cc_final: 0.8299 (tmtt)
REVERT: A 1172 LEU cc_start: 0.7740 (tp) cc_final: 0.7521 (tp)
REVERT: A 1178 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8538 (tm-30)
REVERT: A 1207 GLU cc_start: 0.7556 (tp30) cc_final: 0.7197 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0753
  time to fit residues: 24.1459
Evaluate side-chains
  188 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 51 optimal weight:   20.0000
   chunk 63 optimal weight:    0.1980
   chunk 22 optimal weight:    6.9990
   chunk 91 optimal weight:    9.9990
   chunk 80 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 39 optimal weight:   20.0000
   chunk 6 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 154 GLN
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 805 ASN
A 878 GLN
** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 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 = 0.4084 r_free = 0.4084 target = 0.173231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.135043 restraints weight = 18440.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.136215 restraints weight = 13380.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.137132 restraints weight = 10005.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.138047 restraints weight = 8800.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.138643 restraints weight = 7949.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9215  Z= 0.135
  Angle     :  0.636   8.431  12461  Z= 0.333
  Chirality :  0.043   0.339   1426
  Planarity :  0.004   0.067   1586
  Dihedral  : 10.435 100.255   1289
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.25), residues: 1153
  helix:  1.05 (0.19), residues: 733
  sheet: -0.04 (0.81), residues: 35
  loop : -2.08 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1134 
 TYR   0.015   0.001   TYR A1017 
 PHE   0.024   0.002   PHE A 967 
 TRP   0.041   0.002   TRP A 694 
 HIS   0.003   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9214)
  covalent geometry    : angle       0.63558 (12461)
  hydrogen bonds       : bond        0.04477 (  559)
  hydrogen bonds       : angle       4.40982 ( 1668)
  Misc. bond           : bond        0.00069 (    1)

********************** 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
  219 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 THR cc_start: 0.9502 (p) cc_final: 0.9288 (t)
REVERT: A  103 LEU cc_start: 0.8787 (tp) cc_final: 0.8499 (tp)
REVERT: A  113 TYR cc_start: 0.7084 (t80) cc_final: 0.6770 (t80)
REVERT: A  174 ASP cc_start: 0.8070 (m-30) cc_final: 0.7713 (m-30)
REVERT: A  197 PHE cc_start: 0.8300 (m-80) cc_final: 0.8034 (m-80)
REVERT: A  259 THR cc_start: 0.9662 (p) cc_final: 0.9274 (p)
REVERT: A  263 PHE cc_start: 0.8417 (m-80) cc_final: 0.7847 (m-80)
REVERT: A  364 ILE cc_start: 0.8672 (mp) cc_final: 0.8272 (tp)
REVERT: A  436 MET cc_start: 0.9339 (mmp) cc_final: 0.8981 (mmm)
REVERT: A  485 ARG cc_start: 0.8059 (mtm110) cc_final: 0.7768 (mtm110)
REVERT: A  821 VAL cc_start: 0.8150 (t) cc_final: 0.7609 (m)
REVERT: A  900 PHE cc_start: 0.9265 (t80) cc_final: 0.8947 (t80)
REVERT: A 1006 ARG cc_start: 0.7602 (ttt90) cc_final: 0.7131 (ttt90)
REVERT: A 1010 LYS cc_start: 0.8508 (tmtt) cc_final: 0.8197 (tmtt)
REVERT: A 1172 LEU cc_start: 0.7760 (tp) cc_final: 0.7534 (tp)
REVERT: A 1178 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8511 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 219
  average time/residue: 0.0773
  time to fit residues: 24.5299
Evaluate side-chains
  188 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 110 optimal weight:    5.9990
   chunk 114 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 805 ASN
A 878 GLN
** A1020 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 = 0.4064 r_free = 0.4064 target = 0.171618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.131104 restraints weight = 17316.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.134556 restraints weight = 12221.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.137062 restraints weight = 9265.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.138916 restraints weight = 7466.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.140091 restraints weight = 6292.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9215  Z= 0.136
  Angle     :  0.655  10.284  12461  Z= 0.340
  Chirality :  0.044   0.398   1426
  Planarity :  0.004   0.070   1586
  Dihedral  : 10.335 100.380   1289
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.25), residues: 1153
  helix:  1.08 (0.19), residues: 727
  sheet: -0.02 (0.81), residues: 35
  loop : -2.02 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1134 
 TYR   0.014   0.001   TYR A1017 
 PHE   0.041   0.002   PHE A  78 
 TRP   0.016   0.001   TRP A 158 
 HIS   0.002   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9214)
  covalent geometry    : angle       0.65476 (12461)
  hydrogen bonds       : bond        0.04501 (  559)
  hydrogen bonds       : angle       4.39056 ( 1668)
  Misc. bond           : bond        0.00085 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1395.13 seconds
wall clock time: 24 minutes 49.30 seconds (1489.30 seconds total)