Starting phenix.real_space_refine
on Thu Feb 13 15:20:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zkb_14761/02_2025/7zkb_14761.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zkb_14761/02_2025/7zkb_14761.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zkb_14761/02_2025/7zkb_14761.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zkb_14761/02_2025/7zkb_14761.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zkb_14761/02_2025/7zkb_14761.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zkb_14761/02_2025/7zkb_14761.cif"
  }
  resolution = 4.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    5806      2.51       5
     N    1541      2.21       5
     O    1657      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9043
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1157, 8968
          Classifications: {'peptide': 1157}
          Link IDs: {'PTRANS': 29, 'TRANS': 1127}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 75
          Unusual residues: {'JIZ': 1, 'JJI': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.49, per 1000 atoms: 0.61
  Number of scatterers: 9043
  At special positions: 0
  Unit cell: (77.004, 112.158, 148.149, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1657      8.00
     N    1541      7.00
     C    5806      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.48
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 5 sheets defined
      65.5% alpha, 2.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  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: 2.73

  Time building geometry restraints manager: 2.80 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:             1.840
  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:             0.020
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.110
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.201   9214  Z= 0.564
  Angle     :  1.045  20.208  12461  Z= 0.643
  Chirality :  0.061   0.357   1426
  Planarity :  0.005   0.062   1586
  Dihedral  : 15.447 112.340   3370
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.80 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.26), residues: 1153
  helix:  1.03 (0.20), residues: 711
  sheet: -0.11 (0.83), residues: 42
  loop : -1.74 (0.31), residues: 400

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

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

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 244
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 MET cc_start: 0.7500 (tpp) cc_final: 0.7296 (mmt)
REVERT: A  127 ILE cc_start: 0.8749 (mt) cc_final: 0.8518 (mt)
REVERT: A  152 MET cc_start: 0.7790 (tpp) cc_final: 0.7519 (tmm)
REVERT: A  174 ASP cc_start: 0.7962 (m-30) cc_final: 0.7193 (m-30)
REVERT: A  259 THR cc_start: 0.9561 (p) cc_final: 0.9256 (p)
REVERT: A  263 PHE cc_start: 0.8357 (m-80) cc_final: 0.7986 (m-80)
REVERT: A  316 LEU cc_start: 0.8518 (mt) cc_final: 0.7809 (mt)
REVERT: A  364 ILE cc_start: 0.8642 (mp) cc_final: 0.8133 (tp)
REVERT: A  765 THR cc_start: 0.8773 (m) cc_final: 0.8571 (m)
REVERT: A  913 GLU cc_start: 0.7085 (tt0) cc_final: 0.6694 (tt0)
REVERT: A  968 GLU cc_start: 0.7206 (pp20) cc_final: 0.6880 (pp20)
REVERT: A 1062 LEU cc_start: 0.9358 (tp) cc_final: 0.9077 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 246
  average time/residue: 0.2165
  time to fit residues: 76.8585
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  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    8.9990
   chunk 46 optimal weight:   20.0000
   chunk 90 optimal weight:    3.9990
   chunk 34 optimal weight:   20.0000
   chunk 54 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    2.3986

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.170595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.131091 restraints weight = 18983.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.132531 restraints weight = 14732.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.134419 restraints weight = 10448.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.1559

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

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.25), residues: 1153
  helix:  0.95 (0.20), residues: 707
  sheet:  0.26 (0.85), residues: 35
  loop : -1.76 (0.32), residues: 411

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

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

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 234
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 MET cc_start: 0.8188 (mmm) cc_final: 0.7919 (mmm)
REVERT: A  152 MET cc_start: 0.8081 (tpp) cc_final: 0.7704 (mmm)
REVERT: A  174 ASP cc_start: 0.7807 (m-30) cc_final: 0.7592 (m-30)
REVERT: A  197 PHE cc_start: 0.8323 (m-80) cc_final: 0.8035 (m-80)
REVERT: A  259 THR cc_start: 0.9655 (p) cc_final: 0.9421 (p)
REVERT: A  263 PHE cc_start: 0.8646 (m-80) cc_final: 0.8234 (m-80)
REVERT: A  295 MET cc_start: 0.8004 (ttt) cc_final: 0.7349 (ttt)
REVERT: A  334 VAL cc_start: 0.9094 (t) cc_final: 0.8714 (m)
REVERT: A  436 MET cc_start: 0.9387 (mmp) cc_final: 0.9066 (mmm)
REVERT: A  465 ILE cc_start: 0.8636 (pt) cc_final: 0.8289 (mm)
REVERT: A  533 GLN cc_start: 0.8497 (pt0) cc_final: 0.8284 (tp-100)
REVERT: A  720 LEU cc_start: 0.9523 (mm) cc_final: 0.9317 (mm)
REVERT: A  765 THR cc_start: 0.8917 (m) cc_final: 0.8710 (m)
REVERT: A  796 ASP cc_start: 0.8024 (t0) cc_final: 0.7749 (m-30)
REVERT: A  797 VAL cc_start: 0.8455 (m) cc_final: 0.8003 (t)
REVERT: A  813 ARG cc_start: 0.8201 (tpt170) cc_final: 0.7885 (ttm170)
REVERT: A  821 VAL cc_start: 0.8115 (t) cc_final: 0.7610 (m)
REVERT: A  915 MET cc_start: 0.8132 (mpp) cc_final: 0.7752 (mpp)
REVERT: A  968 GLU cc_start: 0.7572 (pp20) cc_final: 0.7042 (pp20)
REVERT: A 1006 ARG cc_start: 0.7688 (ttt90) cc_final: 0.7314 (ttt90)
REVERT: A 1062 LEU cc_start: 0.9379 (tp) cc_final: 0.9149 (tp)
REVERT: A 1084 ASP cc_start: 0.8803 (p0) cc_final: 0.8599 (p0)
REVERT: A 1209 VAL cc_start: 0.9138 (t) cc_final: 0.8873 (p)
REVERT: A 1211 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8860 (pp30)
  outliers start: 4
  outliers final: 0
  residues processed: 235
  average time/residue: 0.2078
  time to fit residues: 68.7024
Evaluate side-chains
  199 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 583 HIS
A 795 GLN
A 878 GLN
A1103 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.172112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.129949 restraints weight = 18153.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.133364 restraints weight = 12737.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.135843 restraints weight = 9611.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9214  Z= 0.174
  Angle     :  0.598   7.848  12461  Z= 0.318
  Chirality :  0.041   0.161   1426
  Planarity :  0.004   0.061   1586
  Dihedral  : 11.664 105.499   1289
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.70 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.25), residues: 1153
  helix:  1.08 (0.20), residues: 716
  sheet:  0.19 (0.85), residues: 35
  loop : -1.82 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 704 
 HIS   0.006   0.001   HIS A1003 
 PHE   0.024   0.002   PHE A 755 
 TYR   0.020   0.002   TYR A 114 
 ARG   0.004   0.000   ARG A 485 

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

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 225
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.8184 (tpp) cc_final: 0.7459 (mmm)
REVERT: A  174 ASP cc_start: 0.8040 (m-30) cc_final: 0.7683 (m-30)
REVERT: A  259 THR cc_start: 0.9618 (p) cc_final: 0.9256 (p)
REVERT: A  295 MET cc_start: 0.7741 (ttt) cc_final: 0.7127 (ttm)
REVERT: A  436 MET cc_start: 0.9324 (mmp) cc_final: 0.9056 (mmm)
REVERT: A  465 ILE cc_start: 0.8607 (pt) cc_final: 0.8270 (mm)
REVERT: A  533 GLN cc_start: 0.8463 (pt0) cc_final: 0.8180 (tm-30)
REVERT: A  765 THR cc_start: 0.8872 (m) cc_final: 0.8654 (m)
REVERT: A  797 VAL cc_start: 0.8136 (m) cc_final: 0.7558 (t)
REVERT: A  911 LYS cc_start: 0.8002 (ttmm) cc_final: 0.7393 (tttp)
REVERT: A  915 MET cc_start: 0.8151 (mpp) cc_final: 0.7487 (mpp)
REVERT: A  968 GLU cc_start: 0.7463 (pp20) cc_final: 0.6996 (pp20)
REVERT: A 1006 ARG cc_start: 0.7598 (ttt90) cc_final: 0.7298 (ttt90)
REVERT: A 1062 LEU cc_start: 0.9372 (tp) cc_final: 0.9119 (tp)
REVERT: A 1084 ASP cc_start: 0.8688 (p0) cc_final: 0.8448 (p0)
REVERT: A 1111 ILE cc_start: 0.9358 (tt) cc_final: 0.9149 (tt)
  outliers start: 2
  outliers final: 0
  residues processed: 226
  average time/residue: 0.1932
  time to fit residues: 62.6250
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  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 112 optimal weight:    0.8980
   chunk 58 optimal weight:   20.0000
   chunk 41 optimal weight:    9.9990
   chunk 62 optimal weight:    0.5980
   chunk 111 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0980
   chunk 2 optimal weight:    4.9990
   chunk 103 optimal weight:   10.0000
   chunk 56 optimal weight:   40.0000
   chunk 17 optimal weight:    0.6980
   overall best weight:    1.4582

-------------------------------------------------------------------------------
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 452 GLN
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
A 795 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 = 0.4060 r_free = 0.4060 target = 0.170655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.129162 restraints weight = 18255.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.132625 restraints weight = 12579.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.135202 restraints weight = 9426.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9214  Z= 0.198
  Angle     :  0.600   7.662  12461  Z= 0.319
  Chirality :  0.041   0.262   1426
  Planarity :  0.004   0.059   1586
  Dihedral  : 11.316 103.424   1289
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.33 %
    Favored  : 95.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 1153
  helix:  1.18 (0.19), residues: 710
  sheet:  0.19 (0.83), residues: 35
  loop : -1.85 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 704 
 HIS   0.002   0.001   HIS A1003 
 PHE   0.043   0.002   PHE A  78 
 TYR   0.017   0.002   TYR A 243 
 ARG   0.006   0.000   ARG A 534 

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

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 225
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LEU cc_start: 0.8635 (tp) cc_final: 0.8237 (tp)
REVERT: A  154 GLN cc_start: 0.8700 (mt0) cc_final: 0.8467 (tt0)
REVERT: A  174 ASP cc_start: 0.8108 (m-30) cc_final: 0.7694 (m-30)
REVERT: A  259 THR cc_start: 0.9603 (p) cc_final: 0.9032 (p)
REVERT: A  263 PHE cc_start: 0.8359 (m-80) cc_final: 0.7712 (m-80)
REVERT: A  276 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8294 (t0)
REVERT: A  295 MET cc_start: 0.7736 (ttt) cc_final: 0.7204 (ttt)
REVERT: A  334 VAL cc_start: 0.9103 (t) cc_final: 0.8705 (m)
REVERT: A  436 MET cc_start: 0.9355 (mmp) cc_final: 0.9023 (mmm)
REVERT: A  465 ILE cc_start: 0.8571 (pt) cc_final: 0.8280 (mm)
REVERT: A  533 GLN cc_start: 0.8515 (pt0) cc_final: 0.8155 (tm-30)
REVERT: A  765 THR cc_start: 0.8854 (m) cc_final: 0.8618 (m)
REVERT: A  797 VAL cc_start: 0.8584 (m) cc_final: 0.7709 (t)
REVERT: A  915 MET cc_start: 0.8194 (mpp) cc_final: 0.7549 (mpp)
REVERT: A 1006 ARG cc_start: 0.7548 (ttt90) cc_final: 0.7225 (ttt90)
REVERT: A 1062 LEU cc_start: 0.9363 (tp) cc_final: 0.9133 (tp)
REVERT: A 1209 VAL cc_start: 0.9121 (t) cc_final: 0.8865 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 226
  average time/residue: 0.1830
  time to fit residues: 59.7603
Evaluate side-chains
  199 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 48 optimal weight:    0.0070
   chunk 98 optimal weight:    0.6980
   chunk 106 optimal weight:   20.0000
   chunk 45 optimal weight:    4.9990
   chunk 111 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   chunk 82 optimal weight:   10.0000
   chunk 102 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    1.3002

-------------------------------------------------------------------------------
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 805 ASN
A 878 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.172302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.128471 restraints weight = 18848.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.131557 restraints weight = 13384.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.134069 restraints weight = 10335.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9214  Z= 0.189
  Angle     :  0.604   7.856  12461  Z= 0.318
  Chirality :  0.042   0.213   1426
  Planarity :  0.004   0.065   1586
  Dihedral  : 10.986 101.879   1289
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.25), residues: 1153
  helix:  1.25 (0.19), residues: 713
  sheet:  0.34 (0.84), residues: 35
  loop : -1.90 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 704 
 HIS   0.002   0.001   HIS A1151 
 PHE   0.032   0.002   PHE A  78 
 TYR   0.014   0.001   TYR A 243 
 ARG   0.003   0.000   ARG A 794 

*********************** 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
  230 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LEU cc_start: 0.8644 (tp) cc_final: 0.8220 (tp)
REVERT: A  174 ASP cc_start: 0.8093 (m-30) cc_final: 0.7685 (m-30)
REVERT: A  259 THR cc_start: 0.9641 (p) cc_final: 0.8987 (p)
REVERT: A  263 PHE cc_start: 0.8401 (m-80) cc_final: 0.7712 (m-80)
REVERT: A  281 LYS cc_start: 0.8358 (pttp) cc_final: 0.7309 (pttp)
REVERT: A  285 ILE cc_start: 0.9085 (mt) cc_final: 0.8868 (mt)
REVERT: A  295 MET cc_start: 0.7796 (ttt) cc_final: 0.7183 (ttt)
REVERT: A  436 MET cc_start: 0.9387 (mmp) cc_final: 0.9022 (mmm)
REVERT: A  465 ILE cc_start: 0.8580 (pt) cc_final: 0.8294 (mm)
REVERT: A  485 ARG cc_start: 0.7941 (mtm110) cc_final: 0.7606 (mtm110)
REVERT: A  533 GLN cc_start: 0.8573 (pt0) cc_final: 0.8204 (tm-30)
REVERT: A  765 THR cc_start: 0.8773 (m) cc_final: 0.8569 (m)
REVERT: A  797 VAL cc_start: 0.8649 (m) cc_final: 0.7795 (t)
REVERT: A  821 VAL cc_start: 0.8249 (t) cc_final: 0.7679 (m)
REVERT: A  871 GLU cc_start: 0.8155 (tt0) cc_final: 0.7725 (tt0)
REVERT: A  900 PHE cc_start: 0.9124 (t80) cc_final: 0.8669 (t80)
REVERT: A  913 GLU cc_start: 0.7431 (tt0) cc_final: 0.7180 (tt0)
REVERT: A  937 THR cc_start: 0.9244 (t) cc_final: 0.8944 (t)
REVERT: A 1006 ARG cc_start: 0.7574 (ttt90) cc_final: 0.7179 (ttt90)
REVERT: A 1209 VAL cc_start: 0.9103 (t) cc_final: 0.8861 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1918
  time to fit residues: 63.0149
Evaluate side-chains
  196 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 94 optimal weight:   10.0000
   chunk 110 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 109 optimal weight:    9.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
A 276 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 834 GLN
A 878 GLN
A 932 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.162815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.121567 restraints weight = 18317.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.123771 restraints weight = 14068.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.125292 restraints weight = 11473.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   9214  Z= 0.406
  Angle     :  0.767  10.051  12461  Z= 0.423
  Chirality :  0.046   0.195   1426
  Planarity :  0.005   0.065   1586
  Dihedral  : 11.531 102.257   1289
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.27 %
    Favored  : 96.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.25), residues: 1153
  helix:  0.44 (0.19), residues: 716
  sheet: -0.18 (0.79), residues: 35
  loop : -2.01 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP A 704 
 HIS   0.005   0.002   HIS A 149 
 PHE   0.042   0.003   PHE A  71 
 TYR   0.028   0.003   TYR A1017 
 ARG   0.005   0.001   ARG A1134 

*********************** 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  : 0.986 
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  103 LEU cc_start: 0.8802 (tp) cc_final: 0.8255 (tp)
REVERT: A  174 ASP cc_start: 0.8285 (m-30) cc_final: 0.7905 (m-30)
REVERT: A  263 PHE cc_start: 0.8421 (m-80) cc_final: 0.7854 (m-80)
REVERT: A  295 MET cc_start: 0.7990 (ttt) cc_final: 0.7643 (ttt)
REVERT: A  306 TYR cc_start: 0.8211 (t80) cc_final: 0.7915 (t80)
REVERT: A  436 MET cc_start: 0.9382 (mmp) cc_final: 0.9077 (mmm)
REVERT: A  533 GLN cc_start: 0.8650 (pt0) cc_final: 0.8164 (tm-30)
REVERT: A  720 LEU cc_start: 0.9551 (mm) cc_final: 0.9343 (mm)
REVERT: A  766 PHE cc_start: 0.8440 (m-80) cc_final: 0.8210 (m-80)
REVERT: A  821 VAL cc_start: 0.8471 (t) cc_final: 0.7957 (m)
REVERT: A  871 GLU cc_start: 0.8367 (tt0) cc_final: 0.7895 (tt0)
REVERT: A  900 PHE cc_start: 0.9145 (t80) cc_final: 0.8619 (t80)
REVERT: A  913 GLU cc_start: 0.7697 (tt0) cc_final: 0.7327 (tt0)
REVERT: A  915 MET cc_start: 0.8306 (mpp) cc_final: 0.7818 (mpp)
REVERT: A  967 PHE cc_start: 0.8630 (t80) cc_final: 0.8403 (t80)
REVERT: A 1006 ARG cc_start: 0.7532 (ttt90) cc_final: 0.7028 (ttt90)
REVERT: A 1209 VAL cc_start: 0.9202 (t) cc_final: 0.8957 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 227
  average time/residue: 0.2012
  time to fit residues: 64.3860
Evaluate side-chains
  187 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 1.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 99 optimal weight:    0.0670
   chunk 91 optimal weight:    0.8980
   chunk 57 optimal weight:   20.0000
   chunk 111 optimal weight:   20.0000
   chunk 8 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
A 834 GLN
A 878 GLN
** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.170754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.132402 restraints weight = 16967.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.134836 restraints weight = 12674.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.136943 restraints weight = 10090.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9214  Z= 0.187
  Angle     :  0.630   8.223  12461  Z= 0.332
  Chirality :  0.042   0.167   1426
  Planarity :  0.004   0.068   1586
  Dihedral  : 10.727  99.750   1289
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.25), residues: 1153
  helix:  0.97 (0.19), residues: 722
  sheet:  0.03 (0.82), residues: 35
  loop : -1.98 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 694 
 HIS   0.003   0.001   HIS A 514 
 PHE   0.033   0.002   PHE A 755 
 TYR   0.016   0.002   TYR A 243 
 ARG   0.007   0.001   ARG A 485 

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

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 1.057 
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: symmetry clash
REVERT: A  103 LEU cc_start: 0.8679 (tp) cc_final: 0.8224 (tp)
REVERT: A  113 TYR cc_start: 0.7107 (t80) cc_final: 0.6787 (t80)
REVERT: A  174 ASP cc_start: 0.8092 (m-30) cc_final: 0.7678 (m-30)
REVERT: A  259 THR cc_start: 0.9588 (p) cc_final: 0.9076 (p)
REVERT: A  263 PHE cc_start: 0.8378 (m-80) cc_final: 0.7813 (m-80)
REVERT: A  436 MET cc_start: 0.9262 (mmp) cc_final: 0.9020 (mmm)
REVERT: A  485 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7773 (mtm110)
REVERT: A  508 PHE cc_start: 0.6166 (m-10) cc_final: 0.5961 (m-10)
REVERT: A  533 GLN cc_start: 0.8456 (pt0) cc_final: 0.8011 (tm-30)
REVERT: A  720 LEU cc_start: 0.9481 (mm) cc_final: 0.9204 (mm)
REVERT: A  821 VAL cc_start: 0.8266 (t) cc_final: 0.7713 (m)
REVERT: A  871 GLU cc_start: 0.8223 (tt0) cc_final: 0.7698 (tt0)
REVERT: A  900 PHE cc_start: 0.9113 (t80) cc_final: 0.8472 (t80)
REVERT: A  913 GLU cc_start: 0.7357 (tt0) cc_final: 0.7143 (tt0)
REVERT: A  937 THR cc_start: 0.9169 (t) cc_final: 0.8737 (t)
REVERT: A  967 PHE cc_start: 0.8454 (t80) cc_final: 0.8161 (t80)
REVERT: A 1006 ARG cc_start: 0.7428 (ttt90) cc_final: 0.7002 (ttt90)
REVERT: A 1010 LYS cc_start: 0.8469 (tmtt) cc_final: 0.8228 (tmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.2002
  time to fit residues: 64.7545
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  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   chunk 58 optimal weight:    0.0170
   chunk 87 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 101 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 99 optimal weight:    8.9990
   overall best weight:    0.7820

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 367 ASN
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 GLN
A 805 ASN
A 878 GLN
A 932 HIS
** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.170230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.129519 restraints weight = 18139.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.132975 restraints weight = 12596.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.135670 restraints weight = 9469.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9214  Z= 0.187
  Angle     :  0.633   8.316  12461  Z= 0.330
  Chirality :  0.043   0.340   1426
  Planarity :  0.004   0.067   1586
  Dihedral  : 10.401 101.562   1289
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.37 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.25), residues: 1153
  helix:  1.07 (0.19), residues: 720
  sheet:  0.07 (0.82), residues: 35
  loop : -2.03 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A 704 
 HIS   0.005   0.001   HIS A 514 
 PHE   0.032   0.002   PHE A  78 
 TYR   0.026   0.002   TYR A 113 
 ARG   0.006   0.000   ARG A 485 

*********************** 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
  223 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 222
  time to evaluate  : 1.017 
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: 0.9509 (p) cc_final: 0.9300 (t)
REVERT: A  103 LEU cc_start: 0.8759 (tp) cc_final: 0.8157 (tp)
REVERT: A  174 ASP cc_start: 0.8247 (m-30) cc_final: 0.7765 (m-30)
REVERT: A  259 THR cc_start: 0.9626 (p) cc_final: 0.9097 (p)
REVERT: A  263 PHE cc_start: 0.8391 (m-80) cc_final: 0.7817 (m-80)
REVERT: A  285 ILE cc_start: 0.9035 (mt) cc_final: 0.8835 (mt)
REVERT: A  306 TYR cc_start: 0.8204 (t80) cc_final: 0.7885 (t80)
REVERT: A  436 MET cc_start: 0.9357 (mmp) cc_final: 0.9040 (mmm)
REVERT: A  485 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7735 (mtm110)
REVERT: A  533 GLN cc_start: 0.8575 (pt0) cc_final: 0.8126 (tm-30)
REVERT: A  720 LEU cc_start: 0.9465 (mm) cc_final: 0.9214 (mm)
REVERT: A  765 THR cc_start: 0.8808 (m) cc_final: 0.8568 (m)
REVERT: A  794 ARG cc_start: 0.8551 (mmm160) cc_final: 0.8325 (mmm160)
REVERT: A  821 VAL cc_start: 0.8198 (t) cc_final: 0.7696 (m)
REVERT: A  871 GLU cc_start: 0.8251 (tt0) cc_final: 0.7671 (tt0)
REVERT: A  900 PHE cc_start: 0.9196 (t80) cc_final: 0.8488 (t80)
REVERT: A  913 GLU cc_start: 0.7530 (tt0) cc_final: 0.7272 (tt0)
REVERT: A  937 THR cc_start: 0.9294 (t) cc_final: 0.8844 (t)
REVERT: A  967 PHE cc_start: 0.8534 (t80) cc_final: 0.8177 (t80)
REVERT: A  968 GLU cc_start: 0.7810 (pp20) cc_final: 0.7601 (pp20)
REVERT: A 1006 ARG cc_start: 0.7543 (ttt90) cc_final: 0.7083 (ttt90)
REVERT: A 1172 LEU cc_start: 0.7752 (tp) cc_final: 0.7523 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 223
  average time/residue: 0.2011
  time to fit residues: 63.1671
Evaluate side-chains
  195 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 88 optimal weight:    0.8980
   chunk 63 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 93 optimal weight:    0.6980
   chunk 70 optimal weight:    4.9990
   chunk 94 optimal weight:    0.0970
   chunk 96 optimal weight:   30.0000
   chunk 105 optimal weight:    0.6980
   chunk 99 optimal weight:    8.9990
   overall best weight:    0.6578

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.173146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.136558 restraints weight = 17156.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.138865 restraints weight = 11622.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.140580 restraints weight = 8198.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9214  Z= 0.170
  Angle     :  0.622   8.473  12461  Z= 0.326
  Chirality :  0.042   0.313   1426
  Planarity :  0.004   0.068   1586
  Dihedral  : 10.259 101.909   1289
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.25), residues: 1153
  helix:  1.13 (0.19), residues: 722
  sheet:  0.11 (0.82), residues: 35
  loop : -2.06 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP A 704 
 HIS   0.003   0.000   HIS A1003 
 PHE   0.034   0.002   PHE A  78 
 TYR   0.020   0.001   TYR A 113 
 ARG   0.006   0.000   ARG A 485 

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

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 1.016 
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: symmetry clash
REVERT: A   54 THR cc_start: 0.9476 (p) cc_final: 0.9253 (t)
REVERT: A  103 LEU cc_start: 0.8654 (tp) cc_final: 0.8310 (tp)
REVERT: A  114 TYR cc_start: 0.8825 (m-80) cc_final: 0.8530 (m-80)
REVERT: A  174 ASP cc_start: 0.8032 (m-30) cc_final: 0.7670 (m-30)
REVERT: A  259 THR cc_start: 0.9638 (p) cc_final: 0.9120 (p)
REVERT: A  263 PHE cc_start: 0.8320 (m-80) cc_final: 0.7701 (m-80)
REVERT: A  306 TYR cc_start: 0.8174 (t80) cc_final: 0.7876 (t80)
REVERT: A  436 MET cc_start: 0.9321 (mmp) cc_final: 0.9012 (mmm)
REVERT: A  485 ARG cc_start: 0.8027 (mtm110) cc_final: 0.7706 (mtm110)
REVERT: A  533 GLN cc_start: 0.8542 (pt0) cc_final: 0.8092 (tm-30)
REVERT: A  720 LEU cc_start: 0.9461 (mm) cc_final: 0.9177 (mm)
REVERT: A  785 ARG cc_start: 0.8401 (mtt180) cc_final: 0.8079 (ttm110)
REVERT: A  813 ARG cc_start: 0.7721 (tpt170) cc_final: 0.7292 (ttm170)
REVERT: A  821 VAL cc_start: 0.8182 (t) cc_final: 0.7636 (m)
REVERT: A  871 GLU cc_start: 0.8249 (tt0) cc_final: 0.7779 (tt0)
REVERT: A  900 PHE cc_start: 0.9173 (t80) cc_final: 0.8560 (t80)
REVERT: A  937 THR cc_start: 0.9187 (t) cc_final: 0.8829 (t)
REVERT: A  967 PHE cc_start: 0.8499 (t80) cc_final: 0.8081 (t80)
REVERT: A  968 GLU cc_start: 0.7807 (pp20) cc_final: 0.7589 (pp20)
REVERT: A 1006 ARG cc_start: 0.7520 (ttt90) cc_final: 0.7009 (ttt90)
REVERT: A 1172 LEU cc_start: 0.7776 (tp) cc_final: 0.7533 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.2020
  time to fit residues: 63.0902
Evaluate side-chains
  190 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 41 optimal weight:   30.0000
   chunk 64 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 94 optimal weight:    5.9990
   chunk 112 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 70 optimal weight:    9.9990
   chunk 42 optimal weight:    0.7980
   chunk 109 optimal weight:   10.0000
   chunk 58 optimal weight:    7.9990
   overall best weight:    2.4384

-------------------------------------------------------------------------------
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**
** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.168290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.130660 restraints weight = 17367.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.133479 restraints weight = 12672.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.134537 restraints weight = 8538.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   9214  Z= 0.269
  Angle     :  0.694   8.592  12461  Z= 0.377
  Chirality :  0.045   0.316   1426
  Planarity :  0.004   0.063   1586
  Dihedral  : 10.391  99.504   1289
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  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 : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.25), residues: 1153
  helix:  0.95 (0.19), residues: 720
  sheet: -0.17 (0.80), residues: 35
  loop : -2.11 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 704 
 HIS   0.003   0.001   HIS A 141 
 PHE   0.033   0.003   PHE A  78 
 TYR   0.039   0.002   TYR A 114 
 ARG   0.007   0.001   ARG A1134 

********************** 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
  224 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LEU cc_start: 0.8725 (tp) cc_final: 0.8261 (tp)
REVERT: A  174 ASP cc_start: 0.8092 (m-30) cc_final: 0.7661 (m-30)
REVERT: A  259 THR cc_start: 0.9623 (p) cc_final: 0.9182 (p)
REVERT: A  263 PHE cc_start: 0.8348 (m-80) cc_final: 0.7746 (m-80)
REVERT: A  306 TYR cc_start: 0.8330 (t80) cc_final: 0.7690 (t80)
REVERT: A  364 ILE cc_start: 0.8751 (mp) cc_final: 0.8388 (tp)
REVERT: A  436 MET cc_start: 0.9346 (mmp) cc_final: 0.9043 (mmm)
REVERT: A  485 ARG cc_start: 0.8080 (mtm110) cc_final: 0.7759 (mtm110)
REVERT: A  508 PHE cc_start: 0.6291 (m-10) cc_final: 0.6008 (m-10)
REVERT: A  584 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7815 (ttp80)
REVERT: A  720 LEU cc_start: 0.9525 (mm) cc_final: 0.9216 (mm)
REVERT: A  821 VAL cc_start: 0.8350 (t) cc_final: 0.7782 (m)
REVERT: A  871 GLU cc_start: 0.8374 (tt0) cc_final: 0.7857 (tt0)
REVERT: A  900 PHE cc_start: 0.9199 (t80) cc_final: 0.8701 (t80)
REVERT: A  937 THR cc_start: 0.9273 (t) cc_final: 0.8889 (t)
REVERT: A  945 MET cc_start: 0.7741 (ttt) cc_final: 0.7512 (ttt)
REVERT: A  967 PHE cc_start: 0.8677 (t80) cc_final: 0.8166 (t80)
REVERT: A 1006 ARG cc_start: 0.7482 (ttt90) cc_final: 0.6905 (ttt90)
REVERT: A 1172 LEU cc_start: 0.7648 (tp) cc_final: 0.7401 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.1954
  time to fit residues: 62.1225
Evaluate side-chains
  191 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 114 optimal weight:    0.0050
   chunk 95 optimal weight:    8.9990
   chunk 58 optimal weight:    0.0770
   chunk 93 optimal weight:    6.9990
   chunk 34 optimal weight:   20.0000
   chunk 19 optimal weight:    2.9990
   chunk 75 optimal weight:    0.3980
   chunk 27 optimal weight:    0.7980
   chunk 110 optimal weight:    7.9990
   overall best weight:    0.3752

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.174460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.138092 restraints weight = 16313.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.140676 restraints weight = 12015.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.143565 restraints weight = 8284.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9214  Z= 0.173
  Angle     :  0.662   8.794  12461  Z= 0.347
  Chirality :  0.043   0.298   1426
  Planarity :  0.004   0.070   1586
  Dihedral  :  9.946 101.101   1289
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  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 : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.25), residues: 1153
  helix:  1.13 (0.19), residues: 722
  sheet:  0.09 (0.83), residues: 35
  loop : -2.09 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 704 
 HIS   0.004   0.000   HIS A1003 
 PHE   0.023   0.002   PHE A 767 
 TYR   0.029   0.002   TYR A 114 
 ARG   0.006   0.001   ARG A1134 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2755.62 seconds
wall clock time: 50 minutes 21.30 seconds (3021.30 seconds total)