Starting phenix.real_space_refine
on Fri Aug 22 19:53:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n76_24221/08_2025/7n76_24221.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n76_24221/08_2025/7n76_24221.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n76_24221/08_2025/7n76_24221.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n76_24221/08_2025/7n76_24221.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n76_24221/08_2025/7n76_24221.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n76_24221/08_2025/7n76_24221.map"
  }
  resolution = 2.9
  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=   0.001 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      44      5.16       5
     C    4748      2.51       5
     N    1280      2.21       5
     O    1327      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7399
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1036, 7396
          Classifications: {'peptide': 1036}
          Incomplete info: {'truncation_to_alanine': 176}
          Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963}
          Chain breaks: 5
          Unresolved chain link angles: 18
          Unresolved non-hydrogen bonds: 650
          Unresolved non-hydrogen angles: 835
          Unresolved non-hydrogen dihedrals: 549
          Unresolved non-hydrogen chiralities: 59
          Planarities with less than four sites: {'ARG:plan': 21, 'TRP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 14, 'GLN:plan1': 10, 'ASP:plan': 8, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 347
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.64, per 1000 atoms: 0.22
  Number of scatterers: 7399
  At special positions: 0
  Unit cell: (90.214, 102.802, 130.076, 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      44     16.00
     O    1327      8.00
     N    1280      7.00
     C    4748      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 365.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 9 sheets defined
      52.7% alpha, 14.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 57
    Processing helix  chain 'A' and resid 59 through 68
    Processing helix  chain 'A' and resid 68 through 77
      removed outlier: 4.194A  pdb=" N   GLY A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 85
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 188 through 195
    Processing helix  chain 'A' and resid 196 through 198
      No H-bonds generated for 'chain 'A' and resid 196 through 198'
    Processing helix  chain 'A' and resid 200 through 212
      removed outlier: 3.508A  pdb=" N   MET A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   VAL A 206 " --> pdb=" O   GLN A 202 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ARG A 207 " --> pdb=" O   ASP A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 232
    Processing helix  chain 'A' and resid 233 through 249
    Processing helix  chain 'A' and resid 251 through 284
      removed outlier: 3.532A  pdb=" N   SER A 269 " --> pdb=" O   SER A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 393 through 396
    Processing helix  chain 'A' and resid 397 through 408
    Processing helix  chain 'A' and resid 419 through 445
    Processing helix  chain 'A' and resid 448 through 463
      removed outlier: 3.843A  pdb=" N   VAL A 463 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 487
    Processing helix  chain 'A' and resid 492 through 499
      removed outlier: 3.766A  pdb=" N   ASN A 497 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 541
      removed outlier: 4.011A  pdb=" N   ARG A 540 " --> pdb=" O   GLU A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 553
    Processing helix  chain 'A' and resid 566 through 577
    Processing helix  chain 'A' and resid 651 through 659
    Processing helix  chain 'A' and resid 660 through 664
    Processing helix  chain 'A' and resid 667 through 678
      removed outlier: 3.524A  pdb=" N   ALA A 678 " --> pdb=" O   SER A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 701
      removed outlier: 3.704A  pdb=" N   GLN A 701 " --> pdb=" O   GLU A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 709
    Processing helix  chain 'A' and resid 726 through 737
      removed outlier: 3.581A  pdb=" N   VAL A 730 " --> pdb=" O   GLN A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 759
    Processing helix  chain 'A' and resid 821 through 832
    Processing helix  chain 'A' and resid 835 through 842
    Processing helix  chain 'A' and resid 850 through 864
      removed outlier: 3.535A  pdb=" N   THR A 855 " --> pdb=" O   PRO A 851 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU A 864 " --> pdb=" O   GLU A 860 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 877 through 884
    Processing helix  chain 'A' and resid 909 through 949
    Processing helix  chain 'A' and resid 954 through 964
    Processing helix  chain 'A' and resid 964 through 974
      removed outlier: 3.681A  pdb=" N   VAL A 969 " --> pdb=" O   ILE A 965 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   SER A 974 " --> pdb=" O   ALA A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 993 through 1020
      removed outlier: 3.974A  pdb=" N   ALA A1020 " --> pdb=" O   PHE A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1039 through 1061
      removed outlier: 3.827A  pdb=" N   LEU A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1072
    Processing helix  chain 'A' and resid 1073 through 1093
    Processing helix  chain 'A' and resid 1109 through 1145
      Proline residue:  A1138  - end of helix
    Processing helix  chain 'A' and resid 1152 through 1164
      removed outlier: 3.508A  pdb=" N   GLN A1164 " --> pdb=" O   GLU A1160 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37
    Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41
      removed outlier: 4.240A  pdb=" N   ARG A  78 " --> pdb=" O   CYS A  41 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109
      removed outlier: 5.098A  pdb=" N   ARG A 159 " --> pdb=" O   TRP A 170 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA A 176 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 293
    Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315
      removed outlier: 4.533A  pdb=" N   VAL A 386 " --> pdb=" O   LEU A 315 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LEU A 387 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   ASP A 325 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 346 through 350
      removed outlier: 6.660A  pdb=" N   GLU A 332 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   ALA A 378 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   MET A 334 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 490
      removed outlier: 5.975A  pdb=" N   GLY A 887 " --> pdb=" O   PHE A 901 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   SER A 903 " --> pdb=" O   GLY A 887 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   SER A 889 " --> pdb=" O   SER A 903 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   LEU A 504 " --> pdb=" O   GLY A 869 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   ALA A 741 " --> pdb=" O   THR A 844 " (cutoff:3.500A)
      removed outlier: 8.528A  pdb=" N   PHE A 846 " --> pdb=" O   ALA A 741 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   MET A 743 " --> pdb=" O   PHE A 846 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   THR A 844 " --> pdb=" O   ARG A 816 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   LEU A 818 " --> pdb=" O   THR A 844 " (cutoff:3.500A)
      removed outlier: 5.780A  pdb=" N   PHE A 846 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   LEU A 820 " --> pdb=" O   PHE A 846 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   LEU A 768 " --> pdb=" O   MET A 789 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER A 783 " --> pdb=" O   THR A 774 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 519 through 525
      removed outlier: 4.903A  pdb=" N   VAL A 520 " --> pdb=" O   ARG A 720 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ARG A 720 " --> pdb=" O   VAL A 520 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLY A 522 " --> pdb=" O   VAL A 718 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   VAL A 718 " --> pdb=" O   GLY A 522 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   LEU A 713 " --> pdb=" O   SER A 687 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   SER A 687 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   ARG A 631 " --> pdb=" O   PHE A 625 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   PHE A 625 " --> pdb=" O   ARG A 631 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   SER A 633 " --> pdb=" O   PHE A 623 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   ALA A 637 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   VAL A 619 " --> pdb=" O   ALA A 637 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL A 579 " --> pdb=" O   GLY A 591 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 559
      removed outlier: 3.503A  pdb=" N   SER A 557 " --> pdb=" O   VAL A 564 " (cutoff:3.500A)

    454 hydrogen bonds defined for protein.
    1302 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: 1.20

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2163
        1.33 -     1.45: 1028
        1.45 -     1.57: 4280
        1.57 -     1.69: 0
        1.69 -     1.81: 65
  Bond restraints: 7536
  Sorted by residual:
  bond pdb=" CB  VAL A 107 "
       pdb=" CG2 VAL A 107 "
    ideal  model  delta    sigma   weight residual
    1.521  1.349  0.172 3.30e-02 9.18e+02 2.73e+01
  bond pdb=" CB  TYR A 935 "
       pdb=" CG  TYR A 935 "
    ideal  model  delta    sigma   weight residual
    1.512  1.437  0.075 2.20e-02 2.07e+03 1.17e+01
  bond pdb=" C   TYR A 935 "
       pdb=" N   SER A 936 "
    ideal  model  delta    sigma   weight residual
    1.335  1.293  0.042 1.31e-02 5.83e+03 1.02e+01
  bond pdb=" CG  TYR A 935 "
       pdb=" CD1 TYR A 935 "
    ideal  model  delta    sigma   weight residual
    1.389  1.328  0.061 2.10e-02 2.27e+03 8.55e+00
  bond pdb=" CG  GLN A 108 "
       pdb=" CD  GLN A 108 "
    ideal  model  delta    sigma   weight residual
    1.516  1.452  0.064 2.50e-02 1.60e+03 6.54e+00
  ... (remaining 7531 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 10178
        2.28 -     4.57: 108
        4.57 -     6.85: 13
        6.85 -     9.14: 4
        9.14 -    11.42: 1
  Bond angle restraints: 10304
  Sorted by residual:
  angle pdb=" CA  TYR A 935 "
        pdb=" CB  TYR A 935 "
        pdb=" CG  TYR A 935 "
      ideal   model   delta    sigma   weight residual
     113.90  105.40    8.50 1.80e+00 3.09e-01 2.23e+01
  angle pdb=" CG1 VAL A 107 "
        pdb=" CB  VAL A 107 "
        pdb=" CG2 VAL A 107 "
      ideal   model   delta    sigma   weight residual
     110.80  102.10    8.70 2.20e+00 2.07e-01 1.57e+01
  angle pdb=" CB  LEU A 270 "
        pdb=" CG  LEU A 270 "
        pdb=" CD2 LEU A 270 "
      ideal   model   delta    sigma   weight residual
     110.70  122.12  -11.42 3.00e+00 1.11e-01 1.45e+01
  angle pdb=" CA  GLN A 108 "
        pdb=" CB  GLN A 108 "
        pdb=" CG  GLN A 108 "
      ideal   model   delta    sigma   weight residual
     114.10  106.65    7.45 2.00e+00 2.50e-01 1.39e+01
  angle pdb=" N   VAL A 107 "
        pdb=" CA  VAL A 107 "
        pdb=" C   VAL A 107 "
      ideal   model   delta    sigma   weight residual
     107.75  112.37   -4.62 1.46e+00 4.69e-01 1.00e+01
  ... (remaining 10299 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 4191
       17.56 -    35.11: 269
       35.11 -    52.67: 39
       52.67 -    70.23: 6
       70.23 -    87.79: 4
  Dihedral angle restraints: 4509
    sinusoidal: 1516
      harmonic: 2993
  Sorted by residual:
  dihedral pdb=" CA  VAL A 964 "
           pdb=" C   VAL A 964 "
           pdb=" N   ILE A 965 "
           pdb=" CA  ILE A 965 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.37  -18.63     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  LEU A 934 "
           pdb=" C   LEU A 934 "
           pdb=" N   TYR A 935 "
           pdb=" CA  TYR A 935 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.31   16.69     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  SER A 889 "
           pdb=" C   SER A 889 "
           pdb=" N   LEU A 890 "
           pdb=" CA  LEU A 890 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.62  -16.38     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 4506 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.370: 1268
       0.370 -    0.741: 0
       0.741 -    1.111: 0
       1.111 -    1.482: 0
       1.482 -    1.852: 1
  Chirality restraints: 1269
  Sorted by residual:
  chirality pdb=" CG  LEU A 270 "
            pdb=" CB  LEU A 270 "
            pdb=" CD1 LEU A 270 "
            pdb=" CD2 LEU A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.74   -1.85 2.00e-01 2.50e+01 8.58e+01
  chirality pdb=" CA  TYR A 935 "
            pdb=" N   TYR A 935 "
            pdb=" C   TYR A 935 "
            pdb=" CB  TYR A 935 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CG  LEU A 158 "
            pdb=" CB  LEU A 158 "
            pdb=" CD1 LEU A 158 "
            pdb=" CD2 LEU A 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1266 not shown)

  Planarity restraints: 1316
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 934 "   -0.020 2.00e-02 2.50e+03   4.02e-02 1.62e+01
        pdb=" C   LEU A 934 "    0.070 2.00e-02 2.50e+03
        pdb=" O   LEU A 934 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   TYR A 935 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 935 "   -0.028 2.00e-02 2.50e+03   2.77e-02 1.54e+01
        pdb=" CG  TYR A 935 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 935 "    0.052 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 935 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 935 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 935 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 935 "   -0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR A 935 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 107 "    0.013 2.00e-02 2.50e+03   2.57e-02 6.61e+00
        pdb=" C   VAL A 107 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   VAL A 107 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLN A 108 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1313 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 72
        2.64 -     3.20: 7035
        3.20 -     3.77: 11463
        3.77 -     4.33: 15443
        4.33 -     4.90: 26475
  Nonbonded interactions: 60488
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 359 "
            pdb=" OG1 THR A 368 "
     model   vdw
     2.074 3.040
  nonbonded pdb=" OE2 GLU A 172 "
            pdb=" NE2 GLN A 175 "
     model   vdw
     2.159 3.120
  nonbonded pdb=" NH1 ARG A 816 "
            pdb=" O   PRO A1167 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" O   ASP A 325 "
            pdb=" OG1 THR A 391 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   PHE A 958 "
            pdb=" ND2 ASN A 962 "
     model   vdw
     2.311 3.120
  ... (remaining 60483 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 individual isotropic
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:             1.890
  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:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.320
  Find NCS groups from input model:        0.020
  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:6.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
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      :  0.005   0.172   7536  Z= 0.232
  Angle     :  0.643  11.421  10304  Z= 0.341
  Chirality :  0.068   1.852   1269
  Planarity :  0.004   0.063   1316
  Dihedral  : 12.160  87.785   2575
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 aren not related in a simple way.
  whole:  0.22 (0.26), residues: 1024
  helix:  0.65 (0.23), residues: 501
  sheet:  0.25 (0.41), residues: 151
  loop : -0.42 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 281 
 TYR   0.052   0.002   TYR A 935 
 PHE   0.024   0.002   PHE A 958 
 TRP   0.022   0.002   TRP A 100 
 HIS   0.014   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00539 ( 7536)
  covalent geometry    : angle       0.64336 (10304)
  hydrogen bonds       : bond        0.15212 (  454)
  hydrogen bonds       : angle       7.16629 ( 1302)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  761 MET cc_start: 0.8769 (mtt) cc_final: 0.8546 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.5333
  time to fit residues: 28.9221
Evaluate side-chains
  36 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0980
   chunk 51 optimal weight:   40.0000
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 939 GLN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.095229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.067525 restraints weight = 19128.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.80
r_work: 0.3032 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7536  Z= 0.170
  Angle     :  0.590   9.147  10304  Z= 0.294
  Chirality :  0.043   0.183   1269
  Planarity :  0.005   0.056   1316
  Dihedral  :  4.245  17.085   1099
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  4.78 %
    Favored  : 94.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 aren not related in a simple way.
  whole:  0.98 (0.26), residues: 1024
  helix:  1.36 (0.23), residues: 503
  sheet:  0.30 (0.42), residues: 153
  loop : -0.06 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 984 
 TYR   0.022   0.001   TYR A 935 
 PHE   0.023   0.002   PHE A 958 
 TRP   0.006   0.001   TRP A1166 
 HIS   0.002   0.001   HIS A 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 7536)
  covalent geometry    : angle       0.58989 (10304)
  hydrogen bonds       : bond        0.04434 (  454)
  hydrogen bonds       : angle       5.21677 ( 1302)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  379 ARG cc_start: 0.8875 (mmm160) cc_final: 0.8471 (mmm-85)
REVERT: A  421 MET cc_start: 0.8832 (mmp) cc_final: 0.7944 (pp-130)
REVERT: A  761 MET cc_start: 0.9230 (mtt) cc_final: 0.8974 (mtt)
  outliers start: 6
  outliers final: 3
  residues processed: 44
  average time/residue: 0.4325
  time to fit residues: 20.6580
Evaluate side-chains
  39 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue 1031 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 50 optimal weight:   50.0000
   chunk 69 optimal weight:    0.7980
   chunk 44 optimal weight:   50.0000
   chunk 81 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 2 optimal weight:   40.0000
   chunk 75 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 364 HIS
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.093310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.065394 restraints weight = 19255.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.79
r_work: 0.2996 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7536  Z= 0.229
  Angle     :  0.585   9.971  10304  Z= 0.290
  Chirality :  0.044   0.205   1269
  Planarity :  0.004   0.052   1316
  Dihedral  :  4.172  16.665   1099
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  7.88 %
    Favored  : 90.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 aren not related in a simple way.
  whole:  1.21 (0.26), residues: 1024
  helix:  1.54 (0.23), residues: 503
  sheet:  0.21 (0.41), residues: 156
  loop :  0.17 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 984 
 TYR   0.018   0.002   TYR A 935 
 PHE   0.021   0.002   PHE A 958 
 TRP   0.004   0.001   TRP A1166 
 HIS   0.002   0.001   HIS A 772 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 7536)
  covalent geometry    : angle       0.58472 (10304)
  hydrogen bonds       : bond        0.04263 (  454)
  hydrogen bonds       : angle       4.77819 ( 1302)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  421 MET cc_start: 0.8925 (mmp) cc_final: 0.7941 (pp-130)
REVERT: A  521 MET cc_start: 0.5203 (pmm) cc_final: 0.4818 (pmm)
REVERT: A  761 MET cc_start: 0.9198 (mtt) cc_final: 0.8954 (mtt)
  outliers start: 11
  outliers final: 4
  residues processed: 44
  average time/residue: 0.3248
  time to fit residues: 15.8792
Evaluate side-chains
  40 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue 1031 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   chunk 42 optimal weight:    0.3980
   chunk 87 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0980
   chunk 5 optimal weight:    0.5980
   chunk 99 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.095760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.068541 restraints weight = 19659.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.77
r_work: 0.3102 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7536  Z= 0.106
  Angle     :  0.499   7.209  10304  Z= 0.247
  Chirality :  0.041   0.139   1269
  Planarity :  0.004   0.051   1316
  Dihedral  :  3.818  16.463   1099
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  9.14 %
    Favored  : 89.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 aren not related in a simple way.
  whole:  1.64 (0.27), residues: 1024
  helix:  1.95 (0.23), residues: 503
  sheet:  0.23 (0.41), residues: 157
  loop :  0.40 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 740 
 TYR   0.014   0.001   TYR A 935 
 PHE   0.014   0.001   PHE A 940 
 TRP   0.005   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7536)
  covalent geometry    : angle       0.49897 (10304)
  hydrogen bonds       : bond        0.03547 (  454)
  hydrogen bonds       : angle       4.46414 ( 1302)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A  472 MET cc_start: 0.9049 (mmm) cc_final: 0.8836 (mmm)
REVERT: A  521 MET cc_start: 0.5164 (pmm) cc_final: 0.4791 (pmm)
REVERT: A  761 MET cc_start: 0.9147 (mtt) cc_final: 0.8944 (mtt)
REVERT: A 1004 MET cc_start: 0.8747 (mmm) cc_final: 0.8457 (mmm)
  outliers start: 8
  outliers final: 3
  residues processed: 42
  average time/residue: 0.3500
  time to fit residues: 16.1690
Evaluate side-chains
  40 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 MET
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  520 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 60 optimal weight:   20.0000
   chunk 98 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 54 optimal weight:   20.0000
   chunk 37 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.095182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.067471 restraints weight = 19481.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.80
r_work: 0.3092 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7536  Z= 0.125
  Angle     :  0.494   7.286  10304  Z= 0.243
  Chirality :  0.041   0.139   1269
  Planarity :  0.004   0.049   1316
  Dihedral  :  3.674  15.734   1099
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  9.85 %
    Favored  : 88.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 aren not related in a simple way.
  whole:  1.88 (0.27), residues: 1024
  helix:  2.15 (0.23), residues: 503
  sheet:  0.24 (0.41), residues: 151
  loop :  0.56 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 740 
 TYR   0.012   0.001   TYR A 935 
 PHE   0.014   0.001   PHE A 940 
 TRP   0.004   0.001   TRP A 170 
 HIS   0.002   0.000   HIS A 419 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7536)
  covalent geometry    : angle       0.49357 (10304)
  hydrogen bonds       : bond        0.03519 (  454)
  hydrogen bonds       : angle       4.33766 ( 1302)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  199 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8220 (mp)
REVERT: A  472 MET cc_start: 0.9053 (mmm) cc_final: 0.8820 (mmm)
REVERT: A  521 MET cc_start: 0.5435 (OUTLIER) cc_final: 0.4910 (pmm)
REVERT: A  761 MET cc_start: 0.9149 (mtt) cc_final: 0.8896 (mtt)
REVERT: A 1004 MET cc_start: 0.8773 (mmm) cc_final: 0.8498 (mmm)
  outliers start: 10
  outliers final: 3
  residues processed: 45
  average time/residue: 0.3845
  time to fit residues: 18.9585
Evaluate side-chains
  42 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  521 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 101 optimal weight:    0.3980
   chunk 89 optimal weight:    6.9990
   chunk 14 optimal weight:    0.4980
   chunk 60 optimal weight:   20.0000
   chunk 16 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 80 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.095515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.067893 restraints weight = 19531.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.80
r_work: 0.3091 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7536  Z= 0.111
  Angle     :  0.496   8.714  10304  Z= 0.242
  Chirality :  0.040   0.140   1269
  Planarity :  0.004   0.047   1316
  Dihedral  :  3.587  15.732   1099
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 10.41 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 aren not related in a simple way.
  whole:  2.04 (0.27), residues: 1024
  helix:  2.29 (0.23), residues: 503
  sheet:  0.34 (0.40), residues: 162
  loop :  0.62 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 740 
 TYR   0.012   0.001   TYR A 935 
 PHE   0.013   0.001   PHE A 940 
 TRP   0.005   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7536)
  covalent geometry    : angle       0.49568 (10304)
  hydrogen bonds       : bond        0.03363 (  454)
  hydrogen bonds       : angle       4.25289 ( 1302)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  421 MET cc_start: 0.8792 (mmp) cc_final: 0.7760 (pp-130)
REVERT: A  521 MET cc_start: 0.5589 (pmm) cc_final: 0.5020 (pmm)
REVERT: A  761 MET cc_start: 0.9139 (mtt) cc_final: 0.8770 (mtt)
REVERT: A 1004 MET cc_start: 0.8765 (mmm) cc_final: 0.8542 (mmm)
  outliers start: 9
  outliers final: 4
  residues processed: 44
  average time/residue: 0.3619
  time to fit residues: 17.5259
Evaluate side-chains
  41 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue 1031 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 89 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 47 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0370
   chunk 22 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.7862

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.096355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.068984 restraints weight = 19803.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.78
r_work: 0.3100 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7536  Z= 0.117
  Angle     :  0.506   9.471  10304  Z= 0.244
  Chirality :  0.041   0.164   1269
  Planarity :  0.004   0.046   1316
  Dihedral  :  3.541  17.133   1099
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 11.11 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 aren not related in a simple way.
  whole:  2.12 (0.27), residues: 1024
  helix:  2.35 (0.23), residues: 504
  sheet:  0.37 (0.40), residues: 162
  loop :  0.66 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 740 
 TYR   0.011   0.001   TYR A 935 
 PHE   0.013   0.001   PHE A 940 
 TRP   0.003   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7536)
  covalent geometry    : angle       0.50647 (10304)
  hydrogen bonds       : bond        0.03349 (  454)
  hydrogen bonds       : angle       4.23483 ( 1302)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  421 MET cc_start: 0.8766 (mmp) cc_final: 0.7642 (ppp)
REVERT: A  521 MET cc_start: 0.5896 (OUTLIER) cc_final: 0.5421 (pmm)
REVERT: A  761 MET cc_start: 0.9179 (mtt) cc_final: 0.8834 (mtt)
  outliers start: 13
  outliers final: 4
  residues processed: 47
  average time/residue: 0.3365
  time to fit residues: 17.3424
Evaluate side-chains
  43 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  414 PHE
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue 1031 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   chunk 45 optimal weight:   20.0000
   chunk 94 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 73 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.095850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.067038 restraints weight = 19853.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.88
r_work: 0.3061 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7536  Z= 0.158
  Angle     :  0.543  10.387  10304  Z= 0.259
  Chirality :  0.042   0.157   1269
  Planarity :  0.004   0.045   1316
  Dihedral  :  3.607  16.553   1099
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.11 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 aren not related in a simple way.
  whole:  2.09 (0.27), residues: 1024
  helix:  2.29 (0.23), residues: 504
  sheet:  0.43 (0.41), residues: 157
  loop :  0.66 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 740 
 TYR   0.010   0.001   TYR A  40 
 PHE   0.014   0.001   PHE A 940 
 TRP   0.003   0.001   TRP A 301 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 7536)
  covalent geometry    : angle       0.54338 (10304)
  hydrogen bonds       : bond        0.03546 (  454)
  hydrogen bonds       : angle       4.28013 ( 1302)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  421 MET cc_start: 0.8683 (mmp) cc_final: 0.7700 (ptt)
REVERT: A  521 MET cc_start: 0.5972 (OUTLIER) cc_final: 0.5340 (pmm)
REVERT: A  761 MET cc_start: 0.9188 (mtt) cc_final: 0.8812 (mtt)
  outliers start: 10
  outliers final: 5
  residues processed: 45
  average time/residue: 0.3601
  time to fit residues: 17.7610
Evaluate side-chains
  44 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  414 PHE
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue 1031 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0170
   chunk 52 optimal weight:   50.0000
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.7218

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.095460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.068279 restraints weight = 19480.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.77
r_work: 0.3105 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7536  Z= 0.112
  Angle     :  0.516  10.773  10304  Z= 0.246
  Chirality :  0.041   0.173   1269
  Planarity :  0.004   0.044   1316
  Dihedral  :  3.518  15.924   1099
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.67 %
    Favored  : 87.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 aren not related in a simple way.
  whole:  2.16 (0.27), residues: 1024
  helix:  2.37 (0.23), residues: 504
  sheet:  0.40 (0.40), residues: 162
  loop :  0.70 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 740 
 TYR   0.010   0.001   TYR A 161 
 PHE   0.012   0.001   PHE A 940 
 TRP   0.005   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7536)
  covalent geometry    : angle       0.51582 (10304)
  hydrogen bonds       : bond        0.03317 (  454)
  hydrogen bonds       : angle       4.19752 ( 1302)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A  421 MET cc_start: 0.8616 (mmp) cc_final: 0.7656 (ptt)
REVERT: A  521 MET cc_start: 0.5883 (OUTLIER) cc_final: 0.5215 (pmm)
REVERT: A  761 MET cc_start: 0.9167 (mtt) cc_final: 0.8820 (mtt)
  outliers start: 8
  outliers final: 5
  residues processed: 45
  average time/residue: 0.3757
  time to fit residues: 18.4955
Evaluate side-chains
  44 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  414 PHE
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  935 TYR
Chi-restraints excluded: chain A residue 1031 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 87 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 73 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.095279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.068037 restraints weight = 19520.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 2.76
r_work: 0.3099 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7536  Z= 0.120
  Angle     :  0.529  11.535  10304  Z= 0.250
  Chirality :  0.042   0.201   1269
  Planarity :  0.004   0.045   1316
  Dihedral  :  3.497  15.540   1099
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 11.81 %
    Favored  : 87.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 aren not related in a simple way.
  whole:  2.21 (0.27), residues: 1024
  helix:  2.42 (0.23), residues: 504
  sheet:  0.39 (0.41), residues: 157
  loop :  0.72 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 740 
 TYR   0.010   0.001   TYR A 161 
 PHE   0.013   0.001   PHE A 940 
 TRP   0.003   0.001   TRP A 301 
 HIS   0.001   0.000   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7536)
  covalent geometry    : angle       0.52873 (10304)
  hydrogen bonds       : bond        0.03339 (  454)
  hydrogen bonds       : angle       4.19960 ( 1302)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  421 MET cc_start: 0.8557 (mmp) cc_final: 0.7629 (ptt)
REVERT: A  521 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5285 (pmm)
REVERT: A  761 MET cc_start: 0.9174 (mtt) cc_final: 0.8842 (mtt)
  outliers start: 7
  outliers final: 5
  residues processed: 44
  average time/residue: 0.3237
  time to fit residues: 15.5595
Evaluate side-chains
  46 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  414 PHE
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  935 TYR
Chi-restraints excluded: chain A residue 1031 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0050
   chunk 21 optimal weight:    4.9990
   chunk 101 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 97 optimal weight:    0.0040
   chunk 67 optimal weight:    0.1980
   chunk 53 optimal weight:    7.9990
   overall best weight:    0.3806

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1003 GLN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.097363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.070172 restraints weight = 19637.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.77
r_work: 0.3134 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7536  Z= 0.092
  Angle     :  0.507  10.893  10304  Z= 0.240
  Chirality :  0.041   0.231   1269
  Planarity :  0.004   0.044   1316
  Dihedral  :  3.370  16.209   1099
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 12.10 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.23 %
    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 aren not related in a simple way.
  whole:  2.30 (0.27), residues: 1024
  helix:  2.52 (0.23), residues: 505
  sheet:  0.40 (0.41), residues: 157
  loop :  0.73 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 740 
 TYR   0.010   0.001   TYR A 161 
 PHE   0.011   0.001   PHE A 940 
 TRP   0.008   0.001   TRP A 170 
 HIS   0.001   0.000   HIS A 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 7536)
  covalent geometry    : angle       0.50673 (10304)
  hydrogen bonds       : bond        0.03078 (  454)
  hydrogen bonds       : angle       4.09013 ( 1302)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2122.84 seconds
wall clock time: 36 minutes 54.67 seconds (2214.67 seconds total)